ZIP用 VisualBasic 编写的知识图谱数据库引擎 12.75MB

2301_80488214

资源文件列表:

graphQL-main.zip 大约有735个文件
  1. graphQL-main/
  2. graphQL-main/.Rbuildignore 28B
  3. graphQL-main/.Rhistory
  4. graphQL-main/.github/
  5. graphQL-main/.github/ISSUE_TEMPLATE/
  6. graphQL-main/.github/ISSUE_TEMPLATE/bug_report.md 834B
  7. graphQL-main/.github/ISSUE_TEMPLATE/custom.md 126B
  8. graphQL-main/.github/ISSUE_TEMPLATE/feature_request.md 595B
  9. graphQL-main/.github/gpl3.xml 1.05KB
  10. graphQL-main/.github/sync_multiplegit.cmd 155B
  11. graphQL-main/.github/update_banner.cmd 275B
  12. graphQL-main/.gitignore 5.95KB
  13. graphQL-main/.gitmodules 219B
  14. graphQL-main/.pkg/
  15. graphQL-main/.pkg/package.cmd 254B
  16. graphQL-main/.pkg/package_net48.cmd 247B
  17. graphQL-main/.vscode/
  18. graphQL-main/.vscode/settings.json 43B
  19. graphQL-main/@export/
  20. graphQL-main/@export/KnowledgeGraph.d.ts 3.23KB
  21. graphQL-main/@export/MsgFile.d.ts 1.95KB
  22. graphQL-main/@export/Query.d.ts 1.81KB
  23. graphQL-main/@export/graph_mysql.d.ts 2.58KB
  24. graphQL-main/@export/index.d.ts 2.09KB
  25. graphQL-main/@export/mysql.d.ts 5.69KB
  26. graphQL-main/CODE_OF_CONDUCT.md 5.08KB
  27. graphQL-main/DESCRIPTION 369B
  28. graphQL-main/LICENSE 1.06KB
  29. graphQL-main/NAMESPACE 31B
  30. graphQL-main/R/
  31. graphQL-main/R/definition.R 1.44KB
  32. graphQL-main/R/graphKbWeb.R 2.64KB
  33. graphQL-main/R/imports_stopwords.R 5.18KB
  34. graphQL-main/R/text_graph.R 2.81KB
  35. graphQL-main/R/zzz.R 331B
  36. graphQL-main/README.md 1.77KB
  37. graphQL-main/_config.yml 26B
  38. graphQL-main/data/
  39. graphQL-main/data/verbs.txt 2.57KB
  40. graphQL-main/docs/
  41. graphQL-main/docs/1752-0509-8-S4-S11.pdf 837.99KB
  42. graphQL-main/graphQL.Rproj 356B
  43. graphQL-main/man/
  44. graphQL-main/man/.onLoad.1 248B
  45. graphQL-main/man/__cosine.1 338B
  46. graphQL-main/man/__jaccard.1 344B
  47. graphQL-main/man/context_cosine.1 664B
  48. graphQL-main/man/definition.1 773B
  49. graphQL-main/man/get_prompt.1 618B
  50. graphQL-main/man/graphR/
  51. graphQL-main/man/graphR/KnowledgeGraph/
  52. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph.md 756B
  53. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/
  54. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/Kosaraju.SCCs.1 257B
  55. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/as.knowledge.1 422B
  56. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/correctKnowledges.1 347B
  57. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/extractKnowledgeTerms.1 325B
  58. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/graphUMAP.1 269B
  59. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/knowledgeCommunity.1 1.34KB
  60. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/knowledgeIslands.1 353B
  61. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/networkGraph.1 512B
  62. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/niceTerms.1 833B
  63. graphQL-main/man/graphR/KnowledgeGraph/KnowledgeGraph/removeLinkByWeight.1 297B
  64. graphQL-main/man/graphR/MsgFile/
  65. graphQL-main/man/graphR/MsgFile/MsgFile.md 500B
  66. graphQL-main/man/graphR/MsgFile/MsgFile/
  67. graphQL-main/man/graphR/MsgFile/MsgFile/edgeSource.1 239B
  68. graphQL-main/man/graphR/MsgFile/MsgFile/getTerms.1 224B
  69. graphQL-main/man/graphR/MsgFile/MsgFile/open.1 569B
  70. graphQL-main/man/graphR/MsgFile/MsgFile/read.graph.1 433B
  71. graphQL-main/man/graphR/MsgFile/MsgFile/read.knowledge_table.1 495B
  72. graphQL-main/man/graphR/MsgFile/MsgFile/save.1 513B
  73. graphQL-main/man/graphR/MsgFile/MsgFile/seekTerm.1 247B
  74. graphQL-main/man/graphR/Query/
  75. graphQL-main/man/graphR/Query/Query.md 408B
  76. graphQL-main/man/graphR/Query/Query/
  77. graphQL-main/man/graphR/Query/Query/ignore.evidenceLink.1 488B
  78. graphQL-main/man/graphR/Query/Query/insert.1 690B
  79. graphQL-main/man/graphR/Query/Query/join.1 239B
  80. graphQL-main/man/graphR/Query/Query/query.1 480B
  81. graphQL-main/man/graphR/Query/Query/similarity.1 633B
  82. graphQL-main/man/graphR/graph_mysql/
  83. graphQL-main/man/graphR/graph_mysql/graph_mysql.md 575B
  84. graphQL-main/man/graphR/graph_mysql/graph_mysql/
  85. graphQL-main/man/graphR/graph_mysql/graph_mysql/add_term.1 327B
  86. graphQL-main/man/graphR/graph_mysql/graph_mysql/as.knowledge_builder.1 560B
  87. graphQL-main/man/graphR/graph_mysql/graph_mysql/assign_graph.1 543B
  88. graphQL-main/man/graphR/graph_mysql/graph_mysql/fetch_json.1 271B
  89. graphQL-main/man/graphR/graph_mysql/graph_mysql/fetch_table.1 365B
  90. graphQL-main/man/graphR/graph_mysql/graph_mysql/open.graphdb.1 371B
  91. graphQL-main/man/graphR/graph_mysql/graph_mysql/pull_nextGraph.1 582B
  92. graphQL-main/man/graphR/graph_mysql/graph_mysql/save.knowledge.1 766B
  93. graphQL-main/man/graphR/mysql/
  94. graphQL-main/man/graphR/mysql/mysql.md 1.66KB
  95. graphQL-main/man/graphR/mysql/mysql/
  96. graphQL-main/man/graphR/mysql/mysql/add.1 226B
  97. graphQL-main/man/graphR/mysql/mysql/check.1 496B
  98. graphQL-main/man/graphR/mysql/mysql/close_ssh.1 190B
  99. graphQL-main/man/graphR/mysql/mysql/count.1 204B
  100. graphQL-main/man/graphR/mysql/mysql/create_filedump.1 257B
  101. graphQL-main/man/graphR/mysql/mysql/dump_inserts.1 527B
  102. graphQL-main/man/graphR/mysql/mysql/exec.1 455B
  103. graphQL-main/man/graphR/mysql/mysql/find.1 230B
  104. graphQL-main/man/graphR/mysql/mysql/get_last_sql.1 232B
  105. graphQL-main/man/graphR/mysql/mysql/limit.1 269B
  106. graphQL-main/man/graphR/mysql/mysql/open.1 1.13KB
  107. graphQL-main/man/graphR/mysql/mysql/order_by.1 265B
  108. graphQL-main/man/graphR/mysql/mysql/performance_counter.1 1.22KB
  109. graphQL-main/man/graphR/mysql/mysql/project.1 260B
  110. graphQL-main/man/graphR/mysql/mysql/save.1 230B
  111. graphQL-main/man/graphR/mysql/mysql/select.1 238B
  112. graphQL-main/man/graphR/mysql/mysql/table.1 231B
  113. graphQL-main/man/graphR/mysql/mysql/where.1 234B
  114. graphQL-main/man/graphR/mysql/mysql/write_dumps.1 280B
  115. graphQL-main/man/graph_link.1 488B
  116. graphQL-main/man/graph_tokens.1 346B
  117. graphQL-main/man/import_stopwords.1 482B
  118. graphQL-main/man/import_verbs.1 457B
  119. graphQL-main/man/index.json 6.35KB
  120. graphQL-main/man/one_graph.1 602B
  121. graphQL-main/man/push_graph.1 520B
  122. graphQL-main/man/text_graph.1 536B
  123. graphQL-main/man/token_vector.1 633B
  124. graphQL-main/man/tokens_trim.1 334B
  125. graphQL-main/proj_stats.csv 13.24KB
  126. graphQL-main/src/
  127. graphQL-main/src/Capture.PNG 26.29KB
  128. graphQL-main/src/graphMsg/
  129. graphQL-main/src/graphMsg/EvidenceLinks.vb 4.31KB
  130. graphQL-main/src/graphMsg/EvidenceStream.vb 3.79KB
  131. graphQL-main/src/graphMsg/GraphReader.vb 2.98KB
  132. graphQL-main/src/graphMsg/JSONDump.vb 4.43KB
  133. graphQL-main/src/graphMsg/Message/
  134. graphQL-main/src/graphMsg/Message/EvidenceMsg.vb 3.27KB
  135. graphQL-main/src/graphMsg/Message/IndexByRef.vb 1.93KB
  136. graphQL-main/src/graphMsg/Message/KnowledgeMsg.vb 3.39KB
  137. graphQL-main/src/graphMsg/Message/LinkMsg.vb 3.24KB
  138. graphQL-main/src/graphMsg/Message/TermIndexMsg.vb 2.17KB
  139. graphQL-main/src/graphMsg/SeekIndex.vb 6.8KB
  140. graphQL-main/src/graphMsg/StorageProvider.vb 4.62KB
  141. graphQL-main/src/graphMsg/StreamEmit.vb 11.5KB
  142. graphQL-main/src/graphMsg/graphMsg.vbproj 3.29KB
  143. graphQL-main/src/graphMySQL/
  144. graphQL-main/src/graphMySQL/ColorHashCode.vb 3.72KB
  145. graphQL-main/src/graphMySQL/KnowledgeLink.vb 2.12KB
  146. graphQL-main/src/graphMySQL/KnowlegdeBuilder.vb 17KB
  147. graphQL-main/src/graphMySQL/SharedSSHCode/
  148. graphQL-main/src/graphMySQL/SharedSSHCode/SSH.vb 1.1KB
  149. graphQL-main/src/graphMySQL/SharedSSHCode/SharedSSHCode.projitems 645B
  150. graphQL-main/src/graphMySQL/SharedSSHCode/SharedSSHCode.shproj 1.02KB
  151. graphQL-main/src/graphMySQL/SignatureVerifycation.vb 1.66KB
  152. graphQL-main/src/graphMySQL/graphMySQL.vb 8.21KB
  153. graphQL-main/src/graphMySQL/graphMySQL.vbproj 1.19KB
  154. graphQL-main/src/graphMySQL/graphdb/
  155. graphQL-main/src/graphMySQL/graphdb/graph.vb 11.26KB
  156. graphQL-main/src/graphMySQL/graphdb/graphdb.projitems 923B
  157. graphQL-main/src/graphMySQL/graphdb/graphdb.shproj 1.02KB
  158. graphQL-main/src/graphMySQL/graphdb/hash_index.vb 8.67KB
  159. graphQL-main/src/graphMySQL/graphdb/knowledge.vb 13.53KB
  160. graphQL-main/src/graphMySQL/graphdb/knowledge_cache.vb 9.3KB
  161. graphQL-main/src/graphMySQL/graphdb/knowledge_vocabulary.vb 13.09KB
  162. graphQL-main/src/graphMySQL/graphdb/mysql_model.cmd 204B
  163. graphQL-main/src/graphMySQL/graphdbMySQL.vb 2.53KB
  164. graphQL-main/src/graphMySQL/mysql.vb 1.83KB
  165. graphQL-main/src/graphQL.sln 71.73KB
  166. graphQL-main/src/graphQL/
  167. graphQL-main/src/graphQL/Graph/
  168. graphQL-main/src/graphQL/Graph/Association.vb 2.23KB
  169. graphQL-main/src/graphQL/Graph/EvidenceGraph.vb 9.39KB
  170. graphQL-main/src/graphQL/Graph/EvidencePool.vb 6.88KB
  171. graphQL-main/src/graphQL/Graph/GraphActions.vb 5.86KB
  172. graphQL-main/src/graphQL/Graph/GraphModel.vb 2.03KB
  173. graphQL-main/src/graphQL/Graph/GraphPool.vb 9.48KB
  174. graphQL-main/src/graphQL/Graph/Knowledge.vb 3.36KB
  175. graphQL-main/src/graphQL/KnowledgeBuilder/
  176. graphQL-main/src/graphQL/KnowledgeBuilder/CreateKnowledge.vb 8.72KB
  177. graphQL-main/src/graphQL/KnowledgeBuilder/CreateNetwork.vb 5.57KB
  178. graphQL-main/src/graphQL/KnowledgeBuilder/HubAlignment.vb 2.13KB
  179. graphQL-main/src/graphQL/KnowledgeBuilder/KnowledgeAlignment.vb 4.11KB
  180. graphQL-main/src/graphQL/KnowledgeBuilder/KnowledgeFrameRow.vb 4.49KB
  181. graphQL-main/src/graphQL/KnowledgeDescription.vb 2.56KB
  182. graphQL-main/src/graphQL/KnowledgeTerm.vb 5.68KB
  183. graphQL-main/src/graphQL/Relationship.vb 1.52KB
  184. graphQL-main/src/graphQL/graphQL.vbproj 3.09KB
  185. graphQL-main/src/graphR/
  186. graphQL-main/src/graphR/FieldParser.vb 6.94KB
  187. graphQL-main/src/graphR/KnowledgeGraph.vb 16.78KB
  188. graphQL-main/src/graphR/MsgFile.vb 7.69KB
  189. graphQL-main/src/graphR/Query.vb 7.36KB
  190. graphQL-main/src/graphR/graphMySQL.vb 16.27KB
  191. graphQL-main/src/graphR/graphR.vbproj 4.53KB
  192. graphQL-main/src/graphR/mysqlDatabase.vb 20.31KB
  193. graphQL-main/src/graphR/networkGraph/
  194. graphQL-main/src/graphR/networkGraph/umapKnowledge.vb 3.22KB
  195. graphQL-main/src/graphR/zzz.vb 1.56KB
  196. graphQL-main/src/mysqli/
  197. graphQL-main/src/tumblr_inline_mqvdlydGCp1qz4rgp.png 123.39KB
  198. graphQL-main/src/web/
  199. graphQL-main/src/web/.vscode/
  200. graphQL-main/src/web/.vscode/settings.json 38B
  201. graphQL-main/src/web/etc/
  202. graphQL-main/src/web/etc/accessController.php 232B
  203. graphQL-main/src/web/etc/apache_configs/
  204. graphQL-main/src/web/etc/apache_configs/site.conf 600B
  205. graphQL-main/src/web/etc/bootstrap.php 571B
  206. graphQL-main/src/web/etc/config.php 1.47KB
  207. graphQL-main/src/web/etc/httpd.sh 993B
  208. graphQL-main/src/web/etc/php.ini 61.2KB
  209. graphQL-main/src/web/framework/
  210. graphQL-main/src/web/framework/php.NET/
  211. graphQL-main/src/web/mysql/
  212. graphQL-main/src/web/mysql/designer.png 31.02KB
  213. graphQL-main/src/web/mysql/export.cmd 182B
  214. graphQL-main/src/web/mysql/graphdb.mwb 20.42KB
  215. graphQL-main/src/web/mysql/graphdb.sql 7.31KB
  216. graphQL-main/src/web/mysql/graphdb/
  217. graphQL-main/src/web/mysql/graphdb/graph.vb 19.33KB
  218. graphQL-main/src/web/mysql/graphdb/hash_index.vb 14.46KB
  219. graphQL-main/src/web/mysql/graphdb/knowledge.vb 20.36KB
  220. graphQL-main/src/web/mysql/graphdb/knowledge_vocabulary.vb 23.06KB
  221. graphQL-main/src/web/mysql/graphdb_upgrade.sql 7.71KB
  222. graphQL-main/src/web/mysql/graphdb_upgrades.report.md 2.64KB
  223. graphQL-main/src/web/mysql/text_mining.mwb 14.14KB
  224. graphQL-main/src/web/mysql/text_mining.mwb.bak 14.02KB
  225. graphQL-main/src/web/mysql/text_mining.sql 5.2KB
  226. graphQL-main/src/web/mysql/text_mining_current.sql 2.63KB
  227. graphQL-main/src/web/mysql/text_mining_current_upgrades_to_text_mining.schema_compares.report.md 1.22KB
  228. graphQL-main/src/web/mysql/update.cmd 574B
  229. graphQL-main/src/web/readme.txt 37B
  230. graphQL-main/src/web/src/
  231. graphQL-main/src/web/src/.htaccess 217B
  232. graphQL-main/src/web/src/index.php 302B
  233. graphQL-main/src/web/src/manifest.json 300B
  234. graphQL-main/src/web/src/mining.php 6.65KB
  235. graphQL-main/src/web/views/
  236. graphQL-main/src/web/views/index.html
  237. graphQL-main/test/
  238. graphQL-main/test/evidenceGraphTest/
  239. graphQL-main/test/evidenceGraphTest/aspirin.graph 5.42KB
  240. graphQL-main/test/evidenceGraphTest/createDb.py 1.54KB
  241. graphQL-main/test/evidenceGraphTest/graphTest.R 1.12KB
  242. graphQL-main/test/evidenceGraphTest/network/
  243. graphQL-main/test/evidenceGraphTest/network/graph_1.png 30.47KB
  244. graphQL-main/test/evidenceGraphTest/network/graph_1/
  245. graphQL-main/test/evidenceGraphTest/network/graph_1/meta.json 148B
  246. graphQL-main/test/evidenceGraphTest/network/graph_1/network-edges.csv 160B
  247. graphQL-main/test/evidenceGraphTest/network/graph_1/nodes.csv 528B
  248. graphQL-main/test/evidenceGraphTest/network/graph_1_terms.csv 60B
  249. graphQL-main/test/evidenceGraphTest/network/graph_2.png 37.58KB
  250. graphQL-main/test/evidenceGraphTest/network/graph_2/
  251. graphQL-main/test/evidenceGraphTest/network/graph_2/meta.json 148B
  252. graphQL-main/test/evidenceGraphTest/network/graph_2/network-edges.csv 160B
  253. graphQL-main/test/evidenceGraphTest/network/graph_2/nodes.csv 528B
  254. graphQL-main/test/evidenceGraphTest/network/graph_2_terms.csv 60B
  255. graphQL-main/test/evidenceGraphTest/network/graph_3.png 26.87KB
  256. graphQL-main/test/evidenceGraphTest/network/graph_3/
  257. graphQL-main/test/evidenceGraphTest/network/graph_3/meta.json 148B
  258. graphQL-main/test/evidenceGraphTest/network/graph_3/network-edges.csv 93B
  259. graphQL-main/test/evidenceGraphTest/network/graph_3/nodes.csv 404B
  260. graphQL-main/test/evidenceGraphTest/network/graph_3_terms.csv 43B
  261. graphQL-main/test/evidenceGraphTest/network/graph_4.png 26.83KB
  262. graphQL-main/test/evidenceGraphTest/network/graph_4/
  263. graphQL-main/test/evidenceGraphTest/network/graph_4/meta.json 148B
  264. graphQL-main/test/evidenceGraphTest/network/graph_4/network-edges.csv 93B
  265. graphQL-main/test/evidenceGraphTest/network/graph_4/nodes.csv 412B
  266. graphQL-main/test/evidenceGraphTest/network/graph_4_terms.csv 43B
  267. graphQL-main/test/evidenceGraphTest/network/raw.png 44.77KB
  268. graphQL-main/test/evidenceGraphTest/network/raw/
  269. graphQL-main/test/evidenceGraphTest/network/raw/meta.json 148B
  270. graphQL-main/test/evidenceGraphTest/network/raw/network-edges.csv 617B
  271. graphQL-main/test/evidenceGraphTest/network/raw/nodes.csv 386B
  272. graphQL-main/test/evidenceGraphTest/network/raw_terms.csv 162B
  273. graphQL-main/test/getEdgeSource.R 359B
  274. graphQL-main/test/graphTest.R 1.11KB
  275. graphQL-main/test/hash_test.R 2.14KB
  276. graphQL-main/test/joinMultiples/
  277. graphQL-main/test/joinMultiples/exportTables.py 241B
  278. graphQL-main/test/joinMultiples/join.py 205B
  279. graphQL-main/test/joinTest/
  280. graphQL-main/test/joinTest/aspirin.graph 10.29KB
  281. graphQL-main/test/joinTest/aspirin_graph/
  282. graphQL-main/test/joinTest/aspirin_graph/meta.json 148B
  283. graphQL-main/test/joinTest/aspirin_graph/network-edges.csv 17.66KB
  284. graphQL-main/test/joinTest/aspirin_graph/nodes.csv 6.96KB
  285. graphQL-main/test/joinTest/createDb.py 2.18KB
  286. graphQL-main/test/joinTest/dbTest.py 673B
  287. graphQL-main/test/joinTest/kb1.graph 7.57KB
  288. graphQL-main/test/joinTest/kb2.graph 5.21KB
  289. graphQL-main/test/joinTest/knowledges.xls 3.76KB
  290. graphQL-main/test/joinTest/knowledges_raw.xls 3.98KB
  291. graphQL-main/test/joinTest/network_graph.py 406B
  292. graphQL-main/test/knowledges/
  293. graphQL-main/test/knowledges/aspirin.graph 1.02MB
  294. graphQL-main/test/knowledges/aspirin_graph/
  295. graphQL-main/test/knowledges/aspirin_graph/meta.json 148B
  296. graphQL-main/test/knowledges/aspirin_graph/network-edges.csv 17.61KB
  297. graphQL-main/test/knowledges/aspirin_graph/nodes.csv 6.96KB
  298. graphQL-main/test/knowledges/chebi.csv 331B
  299. graphQL-main/test/knowledges/createDb.py 1.93KB
  300. graphQL-main/test/knowledges/dbTest.py 673B
  301. graphQL-main/test/knowledges/graph.svg 85.39KB
  302. graphQL-main/test/knowledges/hmdb.csv 409B
  303. graphQL-main/test/knowledges/isoleucine/
  304. graphQL-main/test/knowledges/isoleucine/chebi.csv 457B
  305. graphQL-main/test/knowledges/isoleucine/hmdb.csv 1.93KB
  306. graphQL-main/test/knowledges/isoleucine/kegg.csv 159B
  307. graphQL-main/test/knowledges/kegg.csv 257B
  308. graphQL-main/test/knowledges/knowledges.xls 3.66KB
  309. graphQL-main/test/knowledges/knowledges_raw.xls 4.29KB
  310. graphQL-main/test/knowledges/leucine/
  311. graphQL-main/test/knowledges/leucine/hmdb.csv 1.11KB
  312. graphQL-main/test/knowledges/leucine/kegg.csv 288B
  313. graphQL-main/test/knowledges/network_graph.py 406B
  314. graphQL-main/test/knowledges/viewdb.py 432B
  315. graphQL-main/test/knowledges/water.csv 195B
  316. graphQL-main/test/knowledges/water_chebi.csv 193B
  317. graphQL-main/test/network/
  318. graphQL-main/test/network/graph_1.png 66.71KB
  319. graphQL-main/test/network/graph_1/
  320. graphQL-main/test/network/graph_1/meta.json 148B
  321. graphQL-main/test/network/graph_1/network-edges.csv 745B
  322. graphQL-main/test/network/graph_1/nodes.csv 2.75KB
  323. graphQL-main/test/network/graph_1_terms.csv 12B
  324. graphQL-main/test/network/graph_2.png 279.14KB
  325. graphQL-main/test/network/graph_2/
  326. graphQL-main/test/network/graph_2/meta.json 148B
  327. graphQL-main/test/network/graph_2/network-edges.csv 6.41KB
  328. graphQL-main/test/network/graph_2/nodes.csv 17.67KB
  329. graphQL-main/test/network/graph_2_terms.csv 12B
  330. graphQL-main/test/network/graph_3.png 113.35KB
  331. graphQL-main/test/network/graph_3/
  332. graphQL-main/test/network/graph_3/meta.json 148B
  333. graphQL-main/test/network/graph_3/network-edges.csv 1.82KB
  334. graphQL-main/test/network/graph_3/nodes.csv 4.83KB
  335. graphQL-main/test/network/graph_3_terms.csv 12B
  336. graphQL-main/test/network/raw.png 305.88KB
  337. graphQL-main/test/network/raw/
  338. graphQL-main/test/network/raw/meta.json 148B
  339. graphQL-main/test/network/raw/network-edges.csv 18.76KB
  340. graphQL-main/test/network/raw/nodes.csv 8.99KB
  341. graphQL-main/test/network/raw_terms.csv
  342. graphQL-main/test/network_graph/
  343. graphQL-main/test/network_graph/cluster.csv 33.02KB
  344. graphQL-main/test/network_graph/clustering.R 557B
  345. graphQL-main/test/network_graph/facebook_combined.txt 834.36KB
  346. graphQL-main/test/network_graph/graph/
  347. graphQL-main/test/network_graph/graph/meta.json 148B
  348. graphQL-main/test/network_graph/graph/network-edges.csv 2.15MB
  349. graphQL-main/test/network_graph/graph/nodes.csv 70.36KB
  350. graphQL-main/test/network_graph/node_types.csv 28.03KB
  351. graphQL-main/vignettes/
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  618. graphQL-main/vignettes/clr/System/Xml/Schema/XmlSchemaSet.html 2.67KB
  619. graphQL-main/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleType.html 4.95KB
  620. graphQL-main/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleTypeContent.html 2.76KB
  621. graphQL-main/vignettes/clr/System/Xml/Schema/XmlSchemaType.html 4.68KB
  622. graphQL-main/vignettes/clr/System/Xml/Schema/XmlSchemaUse.html 2.41KB
  623. graphQL-main/vignettes/clr/System/Xml/Schema/XmlSchemaValidity.html 2.25KB
  624. graphQL-main/vignettes/clr/System/Xml/Schema/XmlTypeCode.html 14.08KB
  625. graphQL-main/vignettes/clr/System/Xml/Serialization/
  626. graphQL-main/vignettes/clr/System/Xml/Serialization/XmlSerializerNamespaces.html 1.41KB
  627. graphQL-main/vignettes/clr/System/Xml/XmlAttribute.html 4.28KB
  628. graphQL-main/vignettes/clr/System/Xml/XmlAttributeCollection.html 1.6KB
  629. graphQL-main/vignettes/clr/System/Xml/XmlCharacterData.html 4.18KB
  630. graphQL-main/vignettes/clr/System/Xml/XmlComment.html 4.17KB
  631. graphQL-main/vignettes/clr/System/Xml/XmlDocument.html 5.24KB
  632. graphQL-main/vignettes/clr/System/Xml/XmlDocumentType.html 4.66KB
  633. graphQL-main/vignettes/clr/System/Xml/XmlElement.html 4.16KB
  634. graphQL-main/vignettes/clr/System/Xml/XmlImplementation.html 1.32KB
  635. graphQL-main/vignettes/clr/System/Xml/XmlLinkedNode.html 4.09KB
  636. graphQL-main/vignettes/clr/System/Xml/XmlNameTable.html 1.3KB
  637. graphQL-main/vignettes/clr/System/Xml/XmlNamedNodeMap.html 1.34KB
  638. graphQL-main/vignettes/clr/System/Xml/XmlNode.html 3.84KB
  639. graphQL-main/vignettes/clr/System/Xml/XmlNodeList.html 1.32KB
  640. graphQL-main/vignettes/clr/System/Xml/XmlNodeType.html 5.4KB
  641. graphQL-main/vignettes/clr/System/Xml/XmlQualifiedName.html 1.38KB
  642. graphQL-main/vignettes/clr/System/Xml/XmlTokenizedType.html 4.47KB
  643. graphQL-main/vignettes/clr/graph/
  644. graphQL-main/vignettes/clr/graph/MySQL/
  645. graphQL-main/vignettes/clr/graph/MySQL/KnowlegdeBuilder.html 3.1KB
  646. graphQL-main/vignettes/clr/graph/MySQL/SignatureVerifycation.html 1.34KB
  647. graphQL-main/vignettes/clr/graph/MySQL/graphMySQL.html 2.56KB
  648. graphQL-main/vignettes/clr/graph/MySQL/graphdbMySQL.html 2.61KB
  649. graphQL-main/vignettes/clr/graph/MySQL/mysql.html 2.81KB
  650. graphQL-main/vignettes/clr/graphQL/
  651. graphQL-main/vignettes/clr/graphQL/Graph/
  652. graphQL-main/vignettes/clr/graphQL/Graph/Association.html 2.31KB
  653. graphQL-main/vignettes/clr/graphQL/Graph/Evidence.html 1.34KB
  654. graphQL-main/vignettes/clr/graphQL/Graph/EvidenceGraph.html 2.39KB
  655. graphQL-main/vignettes/clr/graphQL/Graph/EvidencePool.html 1.37KB
  656. graphQL-main/vignettes/clr/graphQL/Graph/GraphModel.html 2.16KB
  657. graphQL-main/vignettes/clr/graphQL/Graph/GraphPool.html 2.2KB
  658. graphQL-main/vignettes/clr/graphQL/Graph/Knowledge.html 2.38KB
  659. graphQL-main/vignettes/clr/graphQL/KnowledgeDescription.html 1.75KB
  660. graphQL-main/vignettes/clr/graphQL/KnowledgeFrameRow.html 1.63KB
  661. graphQL-main/vignettes/clr/graphQL/Relationship.html 1.86KB
  662. graphQL-main/vignettes/graphR/
  663. graphQL-main/vignettes/graphR/KnowledgeGraph.html 5.09KB
  664. graphQL-main/vignettes/graphR/KnowledgeGraph/
  665. graphQL-main/vignettes/graphR/KnowledgeGraph/Kosaraju.SCCs.html 1.88KB
  666. graphQL-main/vignettes/graphR/KnowledgeGraph/as.knowledge.html 2.02KB
  667. graphQL-main/vignettes/graphR/KnowledgeGraph/correctKnowledges.html 1.87KB
  668. graphQL-main/vignettes/graphR/KnowledgeGraph/extractKnowledgeTerms.html 1.92KB
  669. graphQL-main/vignettes/graphR/KnowledgeGraph/graphUMAP.html 1.73KB
  670. graphQL-main/vignettes/graphR/KnowledgeGraph/knowledgeCommunity.html 2.81KB
  671. graphQL-main/vignettes/graphR/KnowledgeGraph/knowledgeIslands.html 1.99KB
  672. graphQL-main/vignettes/graphR/KnowledgeGraph/networkGraph.html 2.01KB
  673. graphQL-main/vignettes/graphR/KnowledgeGraph/niceTerms.html 2.63KB
  674. graphQL-main/vignettes/graphR/KnowledgeGraph/removeLinkByWeight.html 1.91KB
  675. graphQL-main/vignettes/graphR/MsgFile.html 4.57KB
  676. graphQL-main/vignettes/graphR/MsgFile/
  677. graphQL-main/vignettes/graphR/MsgFile/edgeSource.html 1.66KB
  678. graphQL-main/vignettes/graphR/MsgFile/getTerms.html 1.63KB
  679. graphQL-main/vignettes/graphR/MsgFile/open.html 2.47KB
  680. graphQL-main/vignettes/graphR/MsgFile/read.graph.html 2.06KB
  681. graphQL-main/vignettes/graphR/MsgFile/read.knowledge_table.html 2.07KB
  682. graphQL-main/vignettes/graphR/MsgFile/save.html 2.07KB
  683. graphQL-main/vignettes/graphR/MsgFile/seekTerm.html 1.66KB
  684. graphQL-main/vignettes/graphR/Query.html 4.34KB
  685. graphQL-main/vignettes/graphR/Query/
  686. graphQL-main/vignettes/graphR/Query/ignore.evidenceLink.html 2.02KB
  687. graphQL-main/vignettes/graphR/Query/insert.html 2.22KB
  688. graphQL-main/vignettes/graphR/Query/join.html 1.74KB
  689. graphQL-main/vignettes/graphR/Query/query.html 2.09KB
  690. graphQL-main/vignettes/graphR/Query/similarity.html 2.21KB
  691. graphQL-main/vignettes/graphR/graph_mysql.html 4.76KB
  692. graphQL-main/vignettes/graphR/graph_mysql/
  693. graphQL-main/vignettes/graphR/graph_mysql/add_term.html 1.83KB
  694. graphQL-main/vignettes/graphR/graph_mysql/as.knowledge_builder.html 2.21KB
  695. graphQL-main/vignettes/graphR/graph_mysql/assign_graph.html 2.08KB
  696. graphQL-main/vignettes/graphR/graph_mysql/fetch_json.html 1.68KB
  697. graphQL-main/vignettes/graphR/graph_mysql/fetch_table.html 1.83KB
  698. graphQL-main/vignettes/graphR/graph_mysql/open.graphdb.html 2.03KB
  699. graphQL-main/vignettes/graphR/graph_mysql/pull_nextGraph.html 2.2KB
  700. graphQL-main/vignettes/graphR/graph_mysql/save.knowledge.html 2.2KB
  701. graphQL-main/vignettes/graphR/mysql.html 6.63KB
  702. graphQL-main/vignettes/graphR/mysql/
  703. graphQL-main/vignettes/graphR/mysql/add.html 1.63KB
  704. graphQL-main/vignettes/graphR/mysql/check.html 1.96KB
  705. graphQL-main/vignettes/graphR/mysql/close_ssh.html 1.56KB
  706. graphQL-main/vignettes/graphR/mysql/count.html 1.61KB
  707. graphQL-main/vignettes/graphR/mysql/create_filedump.html 1.83KB
  708. graphQL-main/vignettes/graphR/mysql/dump_inserts.html 1.97KB
  709. graphQL-main/vignettes/graphR/mysql/exec.html 2KB
  710. graphQL-main/vignettes/graphR/mysql/find.html 1.69KB
  711. graphQL-main/vignettes/graphR/mysql/get_last_sql.html 1.65KB
  712. graphQL-main/vignettes/graphR/mysql/limit.html 1.7KB
  713. graphQL-main/vignettes/graphR/mysql/open.html 3.17KB
  714. graphQL-main/vignettes/graphR/mysql/order_by.html 1.72KB
  715. graphQL-main/vignettes/graphR/mysql/performance_counter.html 2.97KB
  716. graphQL-main/vignettes/graphR/mysql/project.html 1.65KB
  717. graphQL-main/vignettes/graphR/mysql/save.html 1.64KB
  718. graphQL-main/vignettes/graphR/mysql/select.html 1.7KB
  719. graphQL-main/vignettes/graphR/mysql/table.html 1.79KB
  720. graphQL-main/vignettes/graphR/mysql/where.html 1.64KB
  721. graphQL-main/vignettes/graphR/mysql/write_dumps.html 1.67KB
  722. graphQL-main/vignettes/index.html 1.79KB
  723. graphQL-main/vignettes/keywords.html 109B
  724. graphQL-main/workflow/
  725. graphQL-main/workflow/assign_stopword_class.R 74B
  726. graphQL-main/workflow/cos_test.R 92B
  727. graphQL-main/workflow/definition_test.R 108B
  728. graphQL-main/workflow/graphQuery 2KB
  729. graphQL-main/workflow/graphQuery.R 1.42KB
  730. graphQL-main/workflow/imports_pubmed.R 344B
  731. graphQL-main/workflow/js_test.js 2.65KB
  732. graphQL-main/workflow/pubmed-Aspirin-set.txt 32.32MB
  733. graphQL-main/workflow/save_text.R 4.96KB
  734. graphQL-main/workflow/save_text2.R 2.64KB
  735. graphQL-main/workflow/text_parser.R 2.6KB

资源介绍:

在脚本中导入R#包，然后创建一个空的图形数据库： import graphQL kb = MsgFile::open()
<link href="/image.php?url=https://csdnimg.cn/release/download_crawler_static/css/base.min.css" rel="stylesheet"/><link href="/image.php?url=https://csdnimg.cn/release/download_crawler_static/css/fancy.min.css" rel="stylesheet"/><link href="/image.php?url=https://csdnimg.cn/release/download_crawler_static/89620325/raw.css" rel="stylesheet"/><div id="sidebar" style="display: none"><div id="outline"></div></div><div class="pf w0 h0" data-page-no="1" id="pf1"><div class="pc pc1 w0 h0"><img alt="" class="bi x0 y0 w1 h1" src="/image.php?url=https://csdnimg.cn/release/download_crawler_static/89620325/bg1.jpg"/><div class="t m0 x1 h2 y1 ff1 fs0 fc0 sc0 ls0 ws0">R<span class="_ _0"></span>E<span class="_ _0"></span>S<span class="_ _0"></span>E<span class="_ _0"></span>A<span class="_ _0"></span>R<span class="_ _0"></span>C<span class="_ _0"></span>H<span class="_ _1"> </span>Open<span class="_ _2"> </span>Access</div><div class="t m1 x2 h3 y2 ff2 fs1 fc1 sc0 ls0 ws0">cytoHubba:<span class="_ _3"> </span><span class="ff3">identifying<span class="_ _3"> </span>hub<span class="_ _3"> </span>objects<span class="_ _3"> </span>and<span class="_ _4"> </span>sub-</span></div><div class="t m1 x2 h3 y3 ff3 fs1 fc1 sc0 ls0 ws0">networks<span class="_ _3"> </span>from<span class="_ _4"> </span>complex<span class="_ _3"> </span>interactome</div><div class="t m2 x2 h4 y4 ff4 fs2 fc1 sc0 ls0 ws0">Chia-Hao<span class="_ _5"> </span>Chin</div><div class="t m3 x3 h5 y5 ff4 fs3 fc1 sc0 ls0 ws0">1<span class="ff5">†</span></div><div class="t m2 x4 h4 y4 ff4 fs2 fc1 sc0 ls0 ws0">,<span class="_ _5"> </span>Shu-Hwa<span class="_ _5"> </span>Chen</div><div class="t m3 x5 h5 y5 ff4 fs3 fc1 sc0 ls0 ws0">2<span class="ff5">†</span></div><div class="t m2 x6 h4 y4 ff4 fs2 fc1 sc0 ls0 ws0">,<span class="_ _5"> </span>Hsin-Hung<span class="_ _5"> </span>Wu</div><div class="t m3 x7 h5 y5 ff4 fs3 fc1 sc0 ls0 ws0">6</div><div class="t m2 x8 h4 y4 ff4 fs2 fc1 sc0 ls0 ws0">,<span class="_ _5"> </span>Chin-Wen<span class="_ _5"> </span>Ho</div><div class="t m3 x9 h5 y5 ff4 fs3 fc1 sc0 ls0 ws0">5</div><div class="t m2 xa h4 y4 ff4 fs2 fc1 sc0 ls0 ws0">,<span class="_ _5"> </span>Ming-Tat<span class="_ _5"> </span>Ko</div><div class="t m3 xb h5 y5 ff4 fs3 fc1 sc0 ls0 ws0">2,6*</div><div class="t m2 xc h4 y4 ff4 fs2 fc1 sc0 ls0 ws0">,<span class="_ _5"> </span>Chung-Yen<span class="_ _5"> </span>Lin</div><div class="t m3 xd h5 y5 ff4 fs3 fc1 sc0 ls0 ws0">2,3,4*</div><div class="t m0 x2 h4 y6 ff6 fs2 fc1 sc0 ls0 ws0">From<span class="_ _5"> </span><span class="ff4">Asia<span class="_ _5"> </span>Pacific<span class="_ _5"> </span>Bioinformatics<span class="_ _5"> </span>Network<span class="_ _6"> </span>(APBioNet)<span class="_ _6"> </span>Thirteenth<span class="_ _5"> </span>International<span class="_ _5"> </span>Conference<span class="_ _5"> </span>on<span class="_ _6"> </span>Bioinformatics</span></div><div class="t m0 x2 h4 y7 ff4 fs2 fc1 sc0 ls0 ws0">(InCoB2014)</div><div class="t m0 x2 h4 y8 ff4 fs2 fc1 sc0 ls0 ws0">Sydney,<span class="_ _5"> </span>Australia.<span class="_ _6"> </span>31<span class="_ _5"> </span>July<span class="_ _5"> </span>-<span class="_ _5"> </span>2<span class="_ _5"> </span>August<span class="_ _6"> </span>2014</div><div class="t m0 xe h6 y9 ff1 fs4 fc1 sc0 ls0 ws0">Abstract</div><div class="t m0 xe h7 ya ff7 fs5 fc1 sc0 ls0 ws0">Background:<span class="_ _6"> </span><span class="ff4">Network<span class="_ _6"> </span>is<span class="_ _6"> </span>a<span class="_ _6"> </span>useful<span class="_ _6"> </span>way<span class="_ _6"> </span>for<span class="_ _6"> </span>presenting<span class="_ _6"> </span>many<span class="_ _6"> </span>types<span class="_ _6"> </span>of<span class="_ _6"> </span>biological<span class="_ _6"> </span>data<span class="_ _6"> </span>including<span class="_ _6"> </span>protein-protein</span></div><div class="t m0 xe h7 yb ff4 fs5 fc1 sc0 ls0 ws0">interactions,<span class="_ _6"> </span>gene<span class="_ _6"> </span>regulations,<span class="_ _6"> </span>cellular<span class="_ _6"> </span>pathways,<span class="_ _6"> </span>and<span class="_ _6"> </span>signal<span class="_ _6"> </span>transducti<span class="_ _7"></span>ons.<span class="_ _6"> </span>We<span class="_ _6"> </span>can<span class="_ _6"> </span>measure<span class="_ _6"> </span>nodes<span class="_ _6"> </span>by<span class="_ _6"> </span>their<span class="_ _6"> </span>network</div><div class="t m0 xe h7 yc ff4 fs5 fc1 sc0 ls0 ws0">features<span class="_ _6"> </span>to<span class="_ _6"> </span>infer<span class="_ _6"> </span>their<span class="_ _6"> </span>importance<span class="_ _6"> </span>in<span class="_ _6"> </span>the<span class="_ _6"> </span>network,<span class="_ _6"> </span>and<span class="_ _6"> </span>it<span class="_ _6"> </span>can<span class="_ _6"> </span>help<span class="_ _8"> </span>us<span class="_ _8"> </span>identify<span class="_ _6"> </span>central<span class="_ _6"> </span>el<span class="_ _7"></span>ements<span class="_ _8"> </span>of<span class="_ _6"> </span>biologi<span class="_ _7"></span>cal</div><div class="t m0 xe h7 yd ff4 fs5 fc1 sc0 ls0 ws0">networks.</div><div class="t m0 xe h7 ye ff7 fs5 fc1 sc0 ls0 ws0">Results:<span class="_ _6"> </span><span class="ff4">We<span class="_ _8"> </span>in<span class="_ _7"></span>troduce<span class="_ _6"> </span>a<span class="_ _8"> </span>novel<span class="_ _6"> </span>Cytosca<span class="_ _7"></span>pe<span class="_ _8"> </span>plugin<span class="_ _6"> </span><span class="ff6">cytoHubba<span class="_ _5"> </span></span>for<span class="_ _8"> </span>ranking<span class="_ _6"> </span>nod<span class="_"> </span>es<span class="_ _6"> </span>in<span class="_ _6"> </span>a<span class="_ _6"> </span>network<span class="_ _6"> </span>by<span class="_ _6"> </span>their<span class="_ _6"> </span>network</span></div><div class="t m0 xe h7 yf ff4 fs5 fc1 sc0 ls0 ws0">features.<span class="_ _6"> </span><span class="ff6">CytoHubba<span class="_ _6"> </span></span>provides<span class="_ _6"> </span>11<span class="_ _6"> </span>topological<span class="_ _6"> </span>analysis<span class="_ _6"> </span>methods<span class="_ _6"> </span>including<span class="_ _6"> </span>Degree,<span class="_ _6"> </span>Edge<span class="_ _6"> </span>Percola<span class="_ _7"></span>ted<span class="_ _8"> </span>Component,</div><div class="t m0 xe h7 y10 ff4 fs5 fc1 sc0 ls0 ws0">Maximum<span class="_ _6"> </span>Neighborhood<span class="_ _6"> </span>Component,<span class="_ _6"> </span>Density<span class="_ _6"> </span>of<span class="_ _6"> </span>Maximum<span class="_ _6"> </span>Neighbo<span class="_ _7"></span>rhood<span class="_ _8"> </span>C<span class="_ _7"></span>omponent,<span class="_ _6"> </span>Maximal<span class="_ _6"> </span>Clique<span class="_ _6"> </span>Centrality</div><div class="t m0 xe h7 y11 ff4 fs5 fc1 sc0 ls0 ws0">and<span class="_ _6"> </span>six<span class="_ _8"> </span>centr<span class="_ _7"></span>alities<span class="_ _6"> </span>(Bottleneck,<span class="_ _6"> </span>EcCentricity,<span class="_ _6"> </span>Closeness,<span class="_ _6"> </span>Radiality,<span class="_ _6"> </span>Betweenness,<span class="_ _6"> </span>and<span class="_ _6"> </span>Stress)<span class="_ _6"> </span>ba<span class="_"> </span>sed<span class="_ _6"> </span>on<span class="_ _6"> </span>shortest<span class="_ _6"> </span>paths.</div><div class="t m0 xe h7 y12 ff4 fs5 fc1 sc0 ls0 ws0">Among<span class="_ _6"> </span>the<span class="_ _6"> </span>eleven<span class="_ _8"> </span>me<span class="_ _7"></span>thods,<span class="_ _6"> </span>the<span class="_ _8"> </span>new<span class="_ _6"> </span>proposed<span class="_ _6"> </span>metho<span class="_ _7"></span>d,<span class="_ _8"> </span>MCC,<span class="_ _6"> </span>has<span class="_ _6"> </span>a<span class="_ _6"> </span>better<span class="_ _6"> </span>performance<span class="_ _6"> </span>on<span class="_ _6"> </span>the<span class="_ _6"> </span>precision<span class="_ _6"> </span>of</div><div class="t m0 xe h7 y13 ff4 fs5 fc1 sc0 ls0 ws0">predicting<span class="_ _6"> </span>essential<span class="_ _6"> </span>proteins<span class="_ _6"> </span>from<span class="_ _6"> </span>the<span class="_ _6"> </span>yeast<span class="_ _6"> </span>PPI<span class="_ _8"> </span>network<span class="_ _7"></span>.</div><div class="t m0 xe h7 y14 ff7 fs5 fc1 sc0 ls0 ws0">Conclusions:<span class="_ _6"> </span><span class="ff6">CytoHubba<span class="_ _6"> </span><span class="ff4">provide<span class="_ _6"> </span>a<span class="_ _6"> </span>user-friendly<span class="_ _6"> </span>interface<span class="_ _6"> </span>to<span class="_ _6"> </span>explore<span class="_ _6"> </span>important<span class="_ _6"> </span>nodes<span class="_ _6"> </span>in<span class="_ _6"> </span>biological<span class="_ _6"> </span>networks.<span class="_ _6"> </span>It</span></span></div><div class="t m0 xe h7 y15 ff4 fs5 fc1 sc0 ls0 ws0">computes<span class="_ _6"> </span>all<span class="_ _6"> </span>eleven<span class="_ _6"> </span>methods<span class="_ _6"> </span>in<span class="_ _8"> </span>one<span class="_ _6"> </span>stop<span class="_ _6"> </span>shopping<span class="_ _6"> </span>way<span class="_"> </span>.<span class="_ _6"> </span>Besides,<span class="_ _6"> </span>research<span class="_ _7"></span>ers<span class="_ _8"> </span>ar<span class="_ _7"></span>e<span class="_ _8"> </span>able<span class="_ _6"> </span>to<span class="_ _6"> </span>combine<span class="_ _6"> </span><span class="ff6">cytoHubba<span class="_ _6"> </span></span>with</div><div class="t m0 xe h7 y16 ff4 fs5 fc1 sc0 ls0 ws0">and<span class="_ _6"> </span>other<span class="_ _8"> </span>plugins<span class="_ _6"> </span>into<span class="_ _6"> </span>a<span class="_ _6"> </span>novel<span class="_ _6"> </span>analysi<span class="_"> </span>s<span class="_ _6"> </span>scheme.<span class="_ _6"> </span>The<span class="_ _6"> </span>network<span class="_ _6"> </span>and<span class="_ _6"> </span>sub-networks<span class="_ _6"> </span>caugh<span class="_ _7"></span>t<span class="_ _8"> </span>by<span class="_ _6"> </span>this<span class="_ _6"> </span>topological<span class="_ _6"> </span>analysis</div><div class="t m0 xe h7 y17 ff4 fs5 fc1 sc0 ls0 ws0">strategy<span class="_ _6"> </span>will<span class="_ _6"> </span>lead<span class="_ _8"> </span>to<span class="_ _6"> </span>new<span class="_ _6"> </span>insights<span class="_ _6"> </span>on<span class="_ _6"> </span>essential<span class="_ _6"> </span>regulatory<span class="_ _6"> </span>networks<span class="_ _6"> </span>and<span class="_ _6"> </span>protein<span class="_ _6"> </span>drug<span class="_ _6"> </span>targets<span class="_ _6"> </span>for<span class="_ _6"> </span>experimental</div><div class="t m0 xe h7 y18 ff4 fs5 fc1 sc0 ls0 ws0">biologists.<span class="_ _6"> </span>According<span class="_ _6"> </span>to<span class="_ _6"> </span>cytoscape<span class="_ _6"> </span>plugin<span class="_ _6"> </span>download<span class="_ _6"> </span>statistics,<span class="_ _6"> </span>the<span class="_ _6"> </span>accumulated<span class="_ _6"> </span>number<span class="_ _6"> </span>of<span class="_ _6"> </span><span class="ff6">cytoHubba<span class="_ _6"> </span></span>is<span class="_ _6"> </span>around</div><div class="t m0 xe h7 y19 ff4 fs5 fc1 sc0 ls0 ws0">6,700<span class="_ _6"> </span>times<span class="_ _6"> </span>since<span class="_ _8"> </span>2010.</div><div class="t m0 x2 h6 y1a ff1 fs4 fc1 sc0 ls0 ws0">Background</div><div class="t m0 x2 h8 y1b ff8 fs6 fc1 sc0 ls1 ws0">Recent<span class="_ _8"> </span>breakthroughs<span class="_ _8"> </span>in<span class="_ _8"> </span>high-throughp<span class="_ _9"></span>ut<span class="_ _8"> </span>techniques</div><div class="t m0 x2 h8 y1c ff8 fs6 fc1 sc0 ls2 ws0">lead<span class="_ _a"> </span>experimental<span class="_ _a"> </span>data<span class="_ _a"> </span>deluges<span class="_ _a"> </span>in<span class="_ _a"> </span>ge<span class="_ _9"></span>nomics,<span class="_ _a"> </span>proteomics,</div><div class="t m0 x2 h8 y1d ff8 fs6 fc1 sc0 ls3 ws0">transcriptomics,<span class="_ _a"> </span>metabolomics<span class="_ _a"> </span>and<span class="_ _a"> </span>interactomics.<span class="_ _a"> </span>These</div><div class="t m0 x2 h8 y1e ff8 fs6 fc1 sc0 ls0 ws0">dat<span class="_ _7"></span>a<span class="_ _a"> </span>ca<span class="_ _7"></span>n<span class="_ _a"> </span>be<span class="_ _8"> </span>rep<span class="_ _7"></span>res<span class="_ _7"></span>ente<span class="_ _7"></span>d<span class="_ _a"> </span>a<span class="_ _7"></span>s<span class="_ _a"> </span>ne<span class="_ _7"></span>two<span class="_"> </span>r<span class="_ _7"></span>ks,<span class="_ _8"> </span>in<span class="_ _a"> </span>w<span class="_ _7"></span>hich<span class="_ _8"> </span>th<span class="_ _7"></span>e<span class="_ _a"> </span>no<span class="_ _7"></span>des</div><div class="t m0 x2 h8 y1f ff8 fs6 fc1 sc0 ls0 ws0">as<span class="_ _a"> </span>surr<span class="_ _7"></span>ogates<span class="_ _8"> </span>for<span class="_ _a"> </span>pro<span class="_ _7"></span>teins,<span class="_ _8"> </span>metabo<span class="_ _7"></span>lites,<span class="_ _a"> </span>o<span class="_ _7"></span>r<span class="_ _a"> </span>trans<span class="_ _7"></span>cripts<span class="_ _7"></span>,<span class="_ _a"> </span>are</div><div class="t m0 x2 h8 y20 ff8 fs6 fc1 sc0 ls4 ws0">connected<span class="_ _a"> </span>by<span class="_ _a"> </span>edges<span class="_ _a"> </span>to<span class="_ _a"> </span>show<span class="_ _a"> </span>the<span class="_ _8"> </span>interactions,<span class="_ _a"> </span>reactions<span class="_ _9"></span>,</div><div class="t m0 x2 h8 y21 ff8 fs6 fc1 sc0 ls5 ws0">or<span class="_ _a"> </span>regulations<span class="_ _a"> </span>among<span class="_ _8"> </span>nodes.<span class="_ _a"> </span>Network<span class="_ _8"> </span>analysis<span class="_ _a"> </span>can<span class="_ _a"> </span>help</div><div class="t m0 x2 h8 y22 ff8 fs6 fc1 sc0 ls0 ws0">us<span class="_ _a"> </span>understa<span class="_ _7"></span>nd<span class="_ _a"> </span>the<span class="_ _a"> </span>fu<span class="_"> </span>nct<span class="_ _7"></span>ion<span class="_ _a"> </span>of<span class="_ _a"> </span>an<span class="_ _8"> </span>individual<span class="_ _a"> </span>no<span class="_ _7"></span>de<span class="_ _a"> </span>and<span class="_ _a"> </span>th<span class="_"> </span>e</div><div class="t m0 x2 h8 y23 ff8 fs6 fc1 sc0 ls0 ws0">collaboration<span class="_ _a"> </span>between<span class="_ _a"> </span>other<span class="_ _a"> </span>nodes.<span class="_ _a"> </span>For<span class="_ _a"> </span>example,<span class="_ _a"> </span>network</div><div class="t m0 x2 h8 y24 ff8 fs6 fc1 sc0 ls0 ws0">cent<span class="_ _7"></span>rali<span class="_ _7"></span>tie<span class="_ _7"></span>s<span class="_ _a"> </span>rank<span class="_ _8"> </span>node<span class="_ _7"></span>s<span class="_ _a"> </span>of<span class="_ _8"> </span>a<span class="_ _a"> </span>bio<span class="_ _7"></span>log<span class="_ _7"></span>ical<span class="_ _8"> </span>netwo<span class="_ _7"></span>rk<span class="_ _a"> </span>a<span class="_ _7"></span>cco<span class="_"> </span>r<span class="_ _7"></span>ding</div><div class="t m0 xf h8 y25 ff8 fs6 fc1 sc0 ls6 ws0">to<span class="_ _a"> </span>a<span class="_ _8"> </span>given<span class="_ _a"> </span>importance<span class="_ _a"> </span>concept,<span class="_ _a"> </span>and<span class="_ _a"> </span>Jeong<span class="_ _a"> </span><span class="ff9 ls7">et<span class="_ _8"> </span>al</span><span class="ls8">.a<span class="_ _b"></span>p<span class="_ _b"></span>p<span class="_ _b"></span>l<span class="_ _b"></span>i<span class="_ _b"></span>e<span class="_ _b"></span>d</span></div><div class="t m0 xf h8 y26 ff8 fs6 fc1 sc0 ls9 ws0">this<span class="_ _a"> </span>method<span class="_ _a"> </span>on<span class="_ _a"> </span>a<span class="_ _a"> </span>protein-protein<span class="_ _a"> </span>interaction<span class="_ _8"> </span>network<span class="_ _a"> </span>of</div><div class="t m0 xf h8 y27 ff8 fs6 fc1 sc0 lsa ws0">baker<span class="ffa ls0">’</span><span class="lsb">s<span class="_ _a"> </span>yeast<span class="_ _8"> </span>(<span class="ff9 lsc">Saccharomyces<span class="_ _a"> </span>cerevisiae</span><span class="lsd">)[<span class="_ _c"></span>1<span class="_ _b"></span>]<span class="_ _b"></span>.T<span class="_ _c"></span>h<span class="_ _b"></span>e<span class="_ _b"></span>yf<span class="_ _c"></span>o<span class="_ _b"></span>u<span class="_ _b"></span>n<span class="_ _b"></span>d</span></span></div><div class="t m0 xf h8 y28 ff8 fs6 fc1 sc0 ls0 ws0">tha<span class="_"> </span>t<span class="_ _8"> </span>the<span class="_ _a"> </span>d<span class="_ _7"></span>egr<span class="_ _7"></span>ee<span class="_ _a"> </span>of<span class="_ _8"> </span>a<span class="_ _a"> </span>pro<span class="_ _7"></span>tein<span class="_ _8"> </span>cor<span class="_ _7"></span>relat<span class="_ _7"></span>es<span class="_ _a"> </span>wi<span class="_ _7"></span>th<span class="_ _a"> </span>t<span class="_ _7"></span>he<span class="_ _a"> </span>es<span class="_ _7"></span>sent<span class="_ _7"></span>ial<span class="_ _7"></span>-</div><div class="t m0 xf h8 y29 ff8 fs6 fc1 sc0 lse ws0">ity<span class="_ _d"> </span>of<span class="_ _d"> </span>its<span class="_ _5"> </span>gene;<span class="_ _d"> </span>in<span class="_ _d"> </span>other<span class="_ _d"> </span>word,<span class="_ _d"> </span>proteins<span class="_ _d"> </span>with<span class="_ _d"> </span>higher</div><div class="t m0 xf h8 y2a ff8 fs6 fc1 sc0 ls0 ws0">degrees<span class="_ _a"> </span>are<span class="_ _a"> </span>more<span class="_ _a"> </span>likely<span class="_ _e"> </span>to<span class="_ _e"> </span>be<span class="_ _a"> </span>essential<span class="_ _a"> </span>proteins.</div><div class="t m0 x10 h8 y2b ff8 fs6 fc1 sc0 lsf ws0">Cytoscape<span class="_ _e"> </span>[2]<span class="_ _a"> </span>is<span class="_ _a"> </span>an<span class="_ _a"> </span>open<span class="_ _a"> </span>platform<span class="_ _e"> </span>with<span class="_ _a"> </span>many<span class="_ _a"> </span>plugins<span class="_ _e"> </span>to</div><div class="t m0 xf h8 y2c ff8 fs6 fc1 sc0 ls10 ws0">expand<span class="_ _a"> </span>both<span class="_ _8"> </span>the<span class="_ _8"> </span>visualization<span class="_ _a"> </span>options<span class="_ _8"> </span>and<span class="_ _8"> </span>the<span class="_ _8"> </span>network</div><div class="t m0 xf h8 y2d ff8 fs6 fc1 sc0 ls0 ws0">anal<span class="_ _9"></span>ysis<span class="_ _e"> </span>powe<span class="_ _9"></span>r.<span class="_ _e"> </span>Via<span class="_ _e"> </span>Cytosc<span class="_ _9"></span>ape,<span class="_ _e"> </span>the<span class="_ _e"> </span>grap<span class="_ _9"></span>hic<span class="_ _9"></span>al<span class="_ _e"> </span>view<span class="_ _e"> </span>of<span class="_ _e"> </span>a<span class="_ _a"> </span>net-</div><div class="t m0 xf h8 y2e ff8 fs6 fc1 sc0 ls0 ws0">work<span class="_ _8"> </span>is<span class="_ _a"> </span>ea<span class="_ _7"></span>sy<span class="_ _a"> </span>ac<span class="_ _7"></span>cessed<span class="_ _7"></span>,<span class="_ _a"> </span>an<span class="_ _7"></span>d<span class="_ _a"> </span>mul<span class="_ _7"></span>tiple<span class="_ _8"> </span>laye<span class="_ _7"></span>rs<span class="_ _a"> </span>o<span class="_"> </span>f<span class="_ _8"> </span>infor<span class="_ _7"></span>matio<span class="_ _7"></span>n</div><div class="t m0 xf h8 y2f ff8 fs6 fc1 sc0 ls0 ws0">including<span class="_ _e"> </span>large-scale,<span class="_ _a"> </span>genome-wise<span class="_ _a"> </span>experiments,<span class="_ _a"> </span>and<span class="_ _a"> </span>pro-</div><div class="t m0 xf h8 y30 ff8 fs6 fc1 sc0 ls11 ws0">tein<span class="_ _a"> </span>function<span class="_ _a"> </span>annotations<span class="_ _8"> </span>can<span class="_ _a"> </span>be<span class="_ _a"> </span>granted<span class="_ _a"> </span>on<span class="_ _8"> </span>the<span class="_ _a"> </span>interac-</div><div class="t m0 xf h8 y31 ff8 fs6 fc1 sc0 ls12 ws0">tome.<span class="_ _a"> </span>Several<span class="_ _8"> </span>Cytoscape<span class="_ _a"> </span>plugins<span class="_ _a"> </span>can<span class="_ _8"> </span>score<span class="_ _a"> </span>and<span class="_ _8"> </span>rank<span class="_ _a"> </span>the</div><div class="t m0 xf h8 y32 ff8 fs6 fc1 sc0 ls0 ws0">nod<span class="_ _9"></span>es<span class="_ _e"> </span>by<span class="_ _e"> </span>networ<span class="_ _9"></span>k<span class="_ _e"> </span>feat<span class="_ _9"></span>ure<span class="_ _9"></span>s.<span class="_ _e"> </span>For<span class="_ _e"> </span>exa<span class="_ _9"></span>mp<span class="_ _9"></span>le,<span class="_ _e"> </span>Netw<span class="_ _9"></span>or<span class="_ _9"></span>kAna<span class="_ _9"></span>ly<span class="_ _9"></span>zer</div><div class="t m0 xf h8 y33 ff8 fs6 fc1 sc0 ls13 ws0">[3]<span class="_ _a"> </span>and<span class="_ _a"> </span>Cen<span class="_ _7"></span>tiScaPe<span class="_ _8"> </span>[4]<span class="_ _a"> </span>computes<span class="_ _8"> </span>various<span class="_ _8"> </span>topological<span class="_ _8"> </span>net-</div><div class="t m0 xf h8 y34 ff8 fs6 fc1 sc0 ls0 ws0">wor<span class="_ _9"></span>k<span class="_ _e"> </span>par<span class="_ _9"></span>ame<span class="_ _9"></span>ter<span class="_ _9"></span>s<span class="_ _e"> </span>for<span class="_ _e"> </span>u<span class="_ _9"></span>ndir<span class="_ _9"></span>ec<span class="_ _9"></span>ted<span class="_ _e"> </span>an<span class="_ _9"></span>d/<span class="_ _e"> </span>or<span class="_ _f"> </span>dir<span class="_ _9"></span>ecte<span class="_ _9"></span>d<span class="_ _f"> </span>netwo<span class="_ _9"></span>rks<span class="_ _9"></span>.</div><div class="t m0 x2 h9 y35 ff4 fs7 fc1 sc0 ls0 ws0">*<span class="_ _f"> </span>Correspondence:<span class="_ _a"> </span>mtko@iis.sinica.edu.tw;<span class="_ _e"> </span>cylin@iis.sinica.edu.tw</div><div class="t m0 x2 h9 y36 ff5 fs7 fc1 sc0 ls0 ws0">†<span class="_ _f"> </span><span class="ff4">Contribu<span class="_ _7"></span>ted<span class="_ _f"> </span>equally</span></div><div class="t m4 x2 ha y37 ff4 fs8 fc1 sc0 ls0 ws0">2</div><div class="t m0 x11 h9 y38 ff4 fs7 fc1 sc0 ls0 ws0">Institute<span class="_ _e"> </span>of<span class="_ _f"> </span>Information<span class="_ _e"> </span>Science,<span class="_ _e"> </span>Academia<span class="_ _e"> </span>Sinica,<span class="_ _e"> </span>No.<span class="_ _e"> </span>128<span class="_ _e"> </span>Academia<span class="_ _f"> </span>Rd.,</div><div class="t m0 x2 h9 y39 ff4 fs7 fc1 sc0 ls0 ws0">Sec.<span class="_ _f"> </span>2,<span class="_ _e"> </span>Taipei<span class="_ _e"> </span>115,<span class="_ _e"> </span>Taiwan</div><div class="t m0 x2 h9 y3a ff4 fs7 fc1 sc0 ls0 ws0">Full<span class="_ _f"> </span>list<span class="_ _e"> </span>of<span class="_ _e"> </span>author<span class="_ _e"> </span>information<span class="_ _e"> </span>is<span class="_ _e"> </span>available<span class="_ _e"> </span>at<span class="_ _f"> </span>the<span class="_ _e"> </span>end<span class="_ _e"> </span>of<span class="_ _e"> </span>the<span class="_ _f"> </span>article</div><div class="t m0 x2 hb y3b ff3 fs9 fc1 sc0 ls0 ws0">Chin<span class="_ _e"> </span><span class="ff2">et<span class="_ _e"> </span>al</span>.<span class="_ _e"> </span><span class="ff2">BMC<span class="_ _a"> </span>Systems<span class="_ _e"> </span>Biology<span class="_ _e"> </span></span>2014,<span class="_ _e"> </span><span class="ff1">8</span>(Suppl<span class="_ _e"> </span>4):S11</div><div class="t m0 x2 hb y3c ff3 fs9 fc1 sc0 ls0 ws0">http://www.biomedcentral.com/1752-0509/8/S4/S<span class="_ _9"></span>11</div><div class="t m5 x12 hc y3d ff4 fsa fc1 sc0 ls14 ws0">©<span class="_ _f"> </span>2014<span class="_ _10"> </span>Chin<span class="_ _10"> </span>et<span class="_ _f"> </span>al.;<span class="_ _10"> </span>licensee<span class="_ _f"> </span>BioMed<span class="_ _10"> </span>Central<span class="_ _f"> </span>Ltd.<span class="_ _10"> </span>This<span class="_ _f"> </span>is<span class="_ _10"> </span>an<span class="_ _f"> </span>Open<span class="_ _10"> </span>Access<span class="_ _f"> </span>article<span class="_ _10"> </span>distributed<span class="_ _f"> </span>under<span class="_ _10"> </span>the<span class="_ _f"> </span>terms<span class="_ _10"> </span>of<span class="_ _f"> </span>the<span class="_ _10"> </span>Creative<span class="_ _10"> </span>Co<span class="_"> </span>mmons</div><div class="t m5 x12 hc y3e ff4 fsa fc1 sc0 ls0 ws0">Attr<span class="_ _7"></span>ibuti<span class="_ _7"></span>on<span class="_ _e"> </span>Lice<span class="_ _7"></span>nse<span class="_ _e"> </span>(htt<span class="_ _7"></span>p://c<span class="_ _7"></span>rea<span class="_ _7"></span>tive<span class="_"> </span>c<span class="_ _7"></span>omm<span class="_ _7"></span>ons.o<span class="_ _7"></span>rg/<span class="_ _7"></span>lice<span class="_ _7"></span>nses<span class="_ _7"></span>/by/<span class="_ _7"></span>4.0<span class="_ _7"></span>),<span class="_ _f"> </span>whi<span class="_ _7"></span>ch<span class="_ _f"> </span>p<span class="_ _7"></span>ermi<span class="_ _7"></span>ts<span class="_ _f"> </span>u<span class="_ _7"></span>nres<span class="_ _7"></span>trict<span class="_ _7"></span>ed<span class="_ _f"> </span>u<span class="_ _7"></span>se,<span class="_ _e"> </span>dis<span class="_ _7"></span>tribu<span class="_ _7"></span>tio<span class="_ _7"></span>n,<span class="_ _f"> </span>an<span class="_ _7"></span>d<span class="_ _f"> </span>re<span class="_"> </span>p<span class="_ _7"></span>rod<span class="_ _7"></span>uctio<span class="_ _7"></span>n<span class="_ _f"> </span>in</div><div class="t m5 x12 hc y3f ff4 fsa fc1 sc0 ls0 ws0">any<span class="_ _e"> </span>mediu<span class="_ _7"></span>m,<span class="_ _f"> </span>p<span class="_ _7"></span>rov<span class="_ _7"></span>ided<span class="_ _e"> </span>the<span class="_ _e"> </span>orig<span class="_ _7"></span>inal<span class="_ _e"> </span>wor<span class="_ _7"></span>k<span class="_ _f"> </span>is<span class="_ _e"> </span>prop<span class="_ _7"></span>erly<span class="_ _e"> </span>cite<span class="_ _7"></span>d.<span class="_ _f"> </span>T<span class="_ _7"></span>he<span class="_ _f"> </span>C<span class="_ _7"></span>reat<span class="_ _7"></span>ive<span class="_ _f"> </span>C<span class="_ _7"></span>omm<span class="_ _7"></span>ons<span class="_ _f"> </span>Pu<span class="_ _7"></span>blic<span class="_ _e"> </span>Dom<span class="_ _7"></span>ain<span class="_ _e"> </span>Ded<span class="_"> </span>ic<span class="_ _7"></span>at<span class="_ _7"></span>ion<span class="_ _f"> </span>w<span class="_ _7"></span>aiv<span class="_"> </span>e<span class="_ _7"></span>r<span class="_ _f"> </span>(h<span class="_ _7"></span>ttp:<span class="_ _7"></span>//</div><div class="t m5 x12 hc y40 ff4 fsa fc1 sc0 ls0 ws0">creat<span class="_ _7"></span>ive<span class="_ _7"></span>com<span class="_"> </span>m<span class="_ _7"></span>ons.<span class="_ _7"></span>org/p<span class="_ _7"></span>ubl<span class="_ _7"></span>icdo<span class="_ _7"></span>main<span class="_ _7"></span>/ze<span class="_ _7"></span>ro/1<span class="_ _7"></span>.0/)<span class="_ _e"> </span>app<span class="_ _7"></span>lies<span class="_ _e"> </span>to<span class="_ _f"> </span>th<span class="_ _7"></span>e<span class="_ _f"> </span>dat<span class="_ _7"></span>a<span class="_ _f"> </span>m<span class="_ _7"></span>ade<span class="_ _f"> </span>av<span class="_ _7"></span>ai<span class="_ _7"></span>labl<span class="_ _7"></span>e<span class="_ _f"> </span>in<span class="_ _e"> </span>this<span class="_ _e"> </span>artic<span class="_ _7"></span>le,<span class="_ _e"> </span>unl<span class="_ _7"></span>ess<span class="_ _e"> </span>othe<span class="_ _7"></span>rwise<span class="_ _e"> </span>stat<span class="_ _7"></span>ed<span class="_ _7"></span>.</div><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a></div><div class="pi" data-data='{"ctm":[1.612697,0.000000,0.000000,1.612697,0.000000,0.000000]}'></div></div><div id="pf2" class="pf w0 h0" data-page-no="2"><div class="pc pc2 w0 h0"><img class="bi x0 y0 w1 h1" alt="" src="/image.php?url=https://csdnimg.cn/release/download_crawler_static/89620325/bg2.jpg"><div class="t m0 x2 h8 y41 ff8 fs6 fc1 sc0 ls15 ws0">These<span class="_ _8"> </span>plugins<span class="_ _8"> </span>provide<span class="_ _8"> </span>more<span class="_ _6"> </span>centrality<span class="_ _8"> </span>measures<span class="_ _8"> </span>than</div><div class="t m0 x2 h8 y42 ff8 fs6 fc1 sc0 ls0 ws0">other<span class="_ _a"> </span>commonly<span class="_ _a"> </span>used,<span class="_ _e"> </span>but<span class="_ _8"> </span>some<span class="_ _a"> </span>other<span class="_ _a"> </span>important<span class="_ _a"> </span>features</div><div class="t m0 x2 h8 y43 ff8 fs6 fc1 sc0 ls0 ws0">and<span class="_ _e"> </span>recent<span class="_ _a"> </span>developed<span class="_ _e"> </span>methods<span class="_ _e"> </span>are<span class="_ _a"> </span>not<span class="_ _a"> </span>included.<span class="_ _e"> </span>Different</div><div class="t m0 x2 h8 y44 ff8 fs6 fc1 sc0 ls0 ws0">methods<span class="_ _e"> </span>focus<span class="_ _e"> </span>on<span class="_ _a"> </span>differen<span class="_ _9"></span>t<span class="_ _a"> </span>topologica<span class="_ _9"></span>l<span class="_ _e"> </span>features,<span class="_ _e"> </span>or<span class="_ _a"> </span>similar</div><div class="t m0 x2 h8 y45 ff8 fs6 fc1 sc0 ls0 ws0">feat<span class="_ _9"></span>ure<span class="_ _9"></span>s<span class="_ _e"> </span>with<span class="_ _e"> </span>diff<span class="_ _9"></span>eren<span class="_ _9"></span>t<span class="_ _e"> </span>scor<span class="_ _9"></span>ing<span class="_ _f"> </span>strate<span class="_ _9"></span>gies<span class="_ _9"></span>.<span class="_ _e"> </span>To<span class="_ _e"> </span>make<span class="_ _f"> </span>the<span class="_ _e"> </span>net-</div><div class="t m0 x2 h8 y46 ff8 fs6 fc1 sc0 ls0 ws0">work<span class="_ _e"> </span>analysis<span class="_ _a"> </span>easier<span class="_ _a"> </span>for<span class="_ _a"> </span>biologists<span class="_ _e"> </span>to<span class="_ _a"> </span>utilize<span class="_ _a"> </span>more<span class="_ _a"> </span>network</div><div class="t m0 x2 h8 y47 ff8 fs6 fc1 sc0 ls16 ws0">features,<span class="_ _a"> </span>we<span class="_ _8"> </span>compose<span class="_ _8"> </span><span class="ff9 ls17">cytoHub<span class="_"> </span>ba<span class="_ _8"> </span></span><span class="ls18">plugin<span class="_ _a"> </span>to<span class="_ _8"> </span>execute<span class="_ _8"> </span>our</span></div><div class="t m0 x2 h8 y48 ff8 fs6 fc1 sc0 ls19 ws0">newly<span class="_ _8"> </span>developed<span class="_ _8"> </span>algorithms<span class="_ _6"> </span>and<span class="_ _8"> </span>several<span class="_ _8"> </span>popular<span class="_ _8"> </span>algo-</div><div class="t m0 x2 h8 y49 ff8 fs6 fc1 sc0 ls17 ws0">rithms.<span class="_ _a"> </span>The<span class="_ _8"> </span>enhanced<span class="_ _8"> </span>node<span class="_ _8"> </span>retrieving<span class="_ _8"> </span>function<span class="_ _a"> </span>in<span class="_ _8"> </span><span class="ff9">cyto-</span></div><div class="t m0 x2 h8 y4a ff9 fs6 fc1 sc0 ls1a ws0">Hubba<span class="_ _8"> </span><span class="ff8 ls1b">control<span class="_ _6"> </span>panel<span class="_ _8"> </span>helps<span class="_ _8"> </span>researchers<span class="_ _8"> </span>to<span class="_ _6"> </span>search<span class="_ _8"> </span>and</span></div><div class="t m0 x2 h8 y4b ff8 fs6 fc1 sc0 ls1c ws0">explore<span class="_ _d"> </span>the<span class="_ _2"> </span>network<span class="_ _2"> </span>and<span class="_ _d"> </span>to<span class="_ _2"> </span>extract<span class="_ _d"> </span>user<span class="_ _2"> </span>interesting</div><div class="t m0 x2 h8 y4c ff8 fs6 fc1 sc0 ls0 ws0">subn<span class="_ _9"></span>etw<span class="_ _9"></span>or<span class="_ _9"></span>k.</div><div class="t m0 x2 h6 y4d ff1 fs4 fc1 sc0 ls0 ws0">Results<span class="_ _6"> </span>and<span class="_ _6"> </span>disc<span class="_ _7"></span>ussion</div><div class="t m0 x2 hd y4e ff7 fsb fc1 sc0 ls0 ws0">The<span class="_ _a"> </span>Usage<span class="_ _8"> </span>of<span class="_ _8"> </span><span class="ffb">cytoHubba</span></div><div class="t m0 x2 h8 y4f ff9 fs6 fc1 sc0 ls1d ws0">CytoHubba<span class="_ _a"> </span><span class="ff8 ls1e">provides<span class="_ _a"> </span>a<span class="_ _8"> </span>simple<span class="_ _a"> </span>interface<span class="_ _a"> </span>to<span class="_ _8"> </span>analyze<span class="_ _a"> </span>a<span class="_ _a"> </span>net-</span></div><div class="t m0 x2 h8 y50 ff8 fs6 fc1 sc0 ls1f ws0">work<span class="_ _a"> </span>with<span class="_ _a"> </span>eleven<span class="_ _8"> </span>scoring<span class="_ _a"> </span>methods.<span class="_ _a"> </span>First,<span class="_ _a"> </span>scores<span class="_ _8"> </span>from<span class="_ _a"> </span>all</div><div class="t m0 x2 h8 y51 ff8 fs6 fc1 sc0 ls9 ws0">eleven<span class="_ _a"> </span>methods<span class="_ _a"> </span>are<span class="_ _a"> </span>granted<span class="_ _8"> </span>to<span class="_ _a"> </span>each<span class="_ _a"> </span>node<span class="_ _8"> </span>in<span class="_ _a"> </span>a<span class="_ _a"> </span>preloaded</div><div class="t m0 x2 h8 y52 ff8 fs6 fc1 sc0 lsc ws0">PPI<span class="_ _a"> </span>network<span class="_ _a"> </span>by<span class="_ _a"> </span>e<span class="_"> </span>xecuting<span class="_ _a"> </span><span class="ffa ls0">&#8220;<span class="_ _7"> </span></span><span class="ls20">compute<span class="_ _a"> </span>hubba<span class="_ _a"> </span>result<span class="ffa ls0">&#8221;<span class="_ _8"> </span></span><span class="ls21">func-</span></span></div><div class="t m0 x2 h8 y53 ff8 fs6 fc1 sc0 ls22 ws0">tion<span class="_ _8"> </span>in<span class="_ _a"> </span>the<span class="_ _8"> </span><span class="ff9 ls15">cytoHubb<span class="_"> </span>a<span class="_ _a"> </span></span><span class="ls23">options<span class="_ _8"> </span>in<span class="_ _8"> </span>cytoscape<span class="_ _8"> </span>menu<span class="_ _8"> </span>bar</span></div><div class="t m0 x2 h8 y54 ff8 fs6 fc1 sc0 ls24 ws0">[plugins].<span class="_ _a"> </span>Next,<span class="_ _a"> </span>top-ranked<span class="_ _a"> </span>nodes<span class="_ _a"> </span>of<span class="_ _a"> </span>a<span class="_ _a"> </span>particular<span class="_ _8"> </span>scoring</div><div class="t m0 xf h8 y55 ff8 fs6 fc1 sc0 ls25 ws0">method<span class="_ _a"> </span>are<span class="_ _a"> </span>retrie<span class="_"> </span>ved<span class="_ _a"> </span>from<span class="_ _8"> </span>the<span class="_ _a"> </span><span class="ff9">cytoHubba<span class="_ _a"> </span></span><span class="ls5">tab<span class="_ _8"> </span>in<span class="_ _a"> </span>Cytos-</span></div><div class="t m0 xf h8 y56 ff8 fs6 fc1 sc0 ls0 ws0">cape<span class="_ _e"> </span>control<span class="_ _a"> </span>panel,<span class="_ _a"> </span>listed<span class="_ _a"> </span>in<span class="_ _a"> </span>the<span class="_ _a"> </span>result<span class="_ _a"> </span>panel,<span class="_ _a"> </span>and<span class="_ _a"> </span>the<span class="_ _a"> </span>sub-</div><div class="t m0 xf h8 y57 ff8 fs6 fc1 sc0 ls0 ws0">graph<span class="_ _e"> </span>of<span class="_ _a"> </span>these<span class="_ _a"> </span>selected<span class="_ _a"> </span>nodes<span class="_ _a"> </span>are<span class="_ _a"> </span>shown<span class="_ _e"> </span>in<span class="_ _a"> </span>the<span class="_ _a"> </span>main<span class="_ _a"> </span>win-</div><div class="t m0 xf h8 y58 ff8 fs6 fc1 sc0 ls26 ws0">dow<span class="_ _a"> </span>with<span class="_ _8"> </span>a<span class="_ _8"> </span>color<span class="_ _a"> </span>scheme<span class="_ _8"> </span>from<span class="_ _a"> </span>h<span class="ls27">ighly<span class="_ _8"> </span>essential<span class="_ _a"> </span>(re<span class="_"> </span>d)<span class="_ _a"> </span>to</span></div><div class="t m0 xf h8 y59 ff8 fs6 fc1 sc0 ls28 ws0">essential<span class="_ _8"> </span>(green).<span class="_ _8"> </span>The<span class="_ _8"> </span>sub-graph<span class="_ _8"> </span>of<span class="_ _8"> </span>essential<span class="_ _a"> </span>nodes<span class="_ _8"> </span>is</div><div class="t m0 xf h8 y5a ff8 fs6 fc1 sc0 ls29 ws0">extendable<span class="_ _8"> </span>to<span class="_ _a"> </span>includ<span class="_"> </span>e<span class="_ _a"> </span>nodes<span class="_ _8"> </span>that<span class="_ _8"> </span>directly<span class="_ _8"> </span>interact<span class="_ _a"> </span>wit<span class="_"> </span>h</div><div class="t m0 xf h8 y5b ff8 fs6 fc1 sc0 ls0 ws0">these<span class="_ _a"> </span>to<span class="_ _7"></span>p-ranked<span class="_ _8"> </span>nodes<span class="_ _a"> </span>by<span class="_ _a"> </span>t<span class="_ _7"></span>he<span class="_ _a"> </span>option<span class="_ _a"> </span>o<span class="_ _7"></span>f<span class="_ _a"> </span><span class="ffa">&#8220;<span class="ff9">check<span class="_ _8"> </span>first<span class="_ _a"> </span>stage</span></span></div><div class="t m0 xf h8 y5c ff9 fs6 fc1 sc0 ls2a ws0">node<span class="ffa ls0">&#8220;<span class="_ _a"> </span><span class="ff8 ls2b">in<span class="_ _a"> </span>control<span class="_ _a"> </span>panel<span class="_ _e"> </span>|<span class="_ _8"> </span>hubba.<span class="_ _e"> </span>Network<span class="_ _a"> </span>topological<span class="_ _a"> </span>fea-</span></span></div><div class="t m0 xf h8 y5d ff8 fs6 fc1 sc0 ls0 ws0">tures<span class="_ _a"> </span>of<span class="_ _a"> </span>nodes<span class="_ _a"> </span>ar<span class="_"> </span>e<span class="_ _a"> </span>re<span class="_ _7"></span>trievable<span class="_ _a"> </span>in<span class="_ _a"> </span>the<span class="_ _a"> </span>data<span class="_ _8"> </span>panel<span class="_ _a"> </span>as<span class="_ _a"> </span>options</div><div class="t m0 xf h8 y5e ff8 fs6 fc1 sc0 ls0 ws0">of<span class="_ _e"> </span>node<span class="_ _a"> </span>attributes.<span class="_ _a"> </span>Tutorials<span class="_ _a"> </span>and<span class="_ _e"> </span>demo<span class="_ _a"> </span>video<span class="_ _a"> </span>are<span class="_ _e"> </span>available</div><div class="t m0 xf h8 y5f ff8 fs6 fc1 sc0 ls2c ws0">in<span class="_ _a"> </span>the<span class="_ _8"> </span>website<span class="_ _8"> </span>(http://hub.iis.sinica.edu.tw/cytohubba).</div><div class="t m0 xf h8 y60 ff8 fs6 fc1 sc0 ls2d ws0">An<span class="_ _a"> </span>example<span class="_ _6"> </span>of<span class="_ _8"> </span><span class="ff9 ls2e">cytoHubba<span class="_ _8"> </span></span><span class="ls2f">result<span class="_ _8"> </span>using<span class="_ _8"> </span>the<span class="_ _8"> </span>Cytoscape</span></div><div class="t m0 xf h8 y61 ff8 fs6 fc1 sc0 ls0 ws0">example<span class="_ _e"> </span>dataset<span class="_ _a"> </span>galFiltered.cys<span class="_ _a"> </span>is<span class="_ _a"> </span>shown<span class="_ _a"> </span>in<span class="_ _e"> </span>Figure<span class="_ _a"> </span>1.</div><div class="t m0 x10 h8 y62 ff9 fs6 fc1 sc0 ls30 ws0">CytoHubba<span class="_ _2"> </span><span class="ff8 ls31">control<span class="_ _d"> </span>panel<span class="_ _2"> </span>is<span class="_ _2"> </span>also<span class="_ _2"> </span>a<span class="_ _2"> </span>handy<span class="_ _d"> </span>tool<span class="_ _2"> </span>to</span></div><div class="t m0 xf h8 y63 ff8 fs6 fc1 sc0 ls32 ws0">retrieve<span class="_ _6"> </span>subnetwork<span class="_ _6"> </span>from<span class="_ _6"> </span>the<span class="_ _6"> </span>whole<span class="_ _6"> </span>big<span class="_ _5"> </span>PPI<span class="_ _6"> </span>set.<span class="_ _6"> </span>A<span class="_ _6"> </span>list</div><div class="t m0 xf h8 y64 ff8 fs6 fc1 sc0 ls33 ws0">of<span class="_ _6"> </span>nodes<span class="_ _6"> </span>can<span class="_ _6"> </span>be<span class="_ _6"> </span>extracted<span class="_ _6"> </span>by<span class="_ _6"> </span>an<span class="_ _6"> </span>ID<span class="_ _6"> </span>list<span class="_ _6"> </span>from<span class="_ _6"> </span>the<span class="_ _6"> </span>whole</div><div class="t m0 xf h8 y65 ff8 fs6 fc1 sc0 ls34 ws0">hubba-computed<span class="_ _6"> </span>network.<span class="_ _5"> </span>This<span class="_ _5"> </span>manipulation<span class="_ _5"> </span>can<span class="_ _5"> </span>be</div><div class="t m0 xf h8 y66 ff8 fs6 fc1 sc0 ls35 ws0">extended<span class="_ _6"> </span>to<span class="_ _5"> </span>include<span class="_ _6"> </span>direct<span class="_ _5"> </span>linking<span class="_ _6"> </span>partners<span class="_ _5"> </span>(check<span class="_ _6"> </span>on</div><div class="t m0 xf h8 y67 ff8 fs6 fc1 sc0 ls36 ws0">the<span class="_ _6"> </span>option<span class="_ _5"> </span><span class="ffc ls0">&#8220;<span class="ff9 ls37">check<span class="_ _5"> </span>first<span class="_ _6"> </span>st<span class="_"> </span>age<span class="_ _6"> </span>node</span>&#8221;<span class="_ _7"> </span></span><span class="ls38">),<span class="_ _5"> </span>saved,<span class="_ _6"> </span>and<span class="_ _6"> </span>re-sub-</span></div><div class="t m0 xf h8 y68 ff8 fs6 fc1 sc0 ls0 ws0">mitted<span class="_ _8"> </span>to<span class="_ _6"> </span><span class="ff9">cytoHubba<span class="_ _6"> </span></span>to<span class="_ _6"> </span>evaluate<span class="_ _6"> </span>the<span class="_ _8"> </span>node<span class="_ _6"> </span>essentiality<span class="_ _6"> </span>on</div><div class="t m0 xf h8 y69 ff8 fs6 fc1 sc0 ls39 ws0">the<span class="_ _d"> </span>selected<span class="_ _d"> </span>sub-network.<span class="_ _d"> </span>For<span class="_ _d"> </span>th<span class="_"> </span>ose<span class="_ _5"> </span>nodes<span class="_ _d"> </span>with<span class="_ _d"> </span>no</div><div class="t m0 xe he y6a ff1 fs9 fc1 sc0 ls3a ws0">Figure<span class="_ _a"> </span>1<span class="_ _a"> </span><span class="ff7 ls3b">T<span class="_"> </span>wo<span class="_ _a"> </span>s<span class="_"> </span>cree<span class="_"> </span>n-sh<span class="_"> </span>ots<span class="_ _8"> </span>showing<span class="_ _8"> </span>centra<span class="_"> </span>lity<span class="_ _8"> </span>analysi<span class="_"> </span>s<span class="_ _a"> </span>wi<span class="_"> </span>th<span class="_ _8"> </span>cytoHu<span class="_"> </span>bba<span class="ff4 ls3c">.(<span class="_ _b"></span>A<span class="_ _b"></span>)A<span class="ffb ls3d">cytoHubba<span class="_ _a"> </span></span><span class="ls3e">analysis<span class="_ _a"> </span>result<span class="_ _8"> </span>using<span class="_ _e"> </span>the<span class="_ _8"> </span>example<span class="_ _e"> </span>dataset</span></span></span></div><div class="t m0 xe he y6b ff4 fs9 fc1 sc0 ls0 ws0">galFiltered.cys<span class="_ _e"> </span>in<span class="_ _e"> </span>the<span class="_ _e"> </span>Cytoscape.<span class="_ _e"> </span>After<span class="_ _e"> </span>the<span class="_ _a"> </span>calculation<span class="_ _e"> </span>(from<span class="_ _e"> </span>the<span class="_ _e"> </span>Cytoscape<span class="_ _e"> </span>menu<span class="_ _a"> </span>bar<span class="_ _e"> </span>[plugins]<span class="_ _e"> </span><span class="ffd">&#174;<span class="_ _e"> </span></span>cytoHubba<span class="_ _a"> </span><span class="ffd">&#174;<span class="_ _e"> </span></span>compute<span class="_ _e"> </span>hubba<span class="_ _e"> </span>result),<span class="_ _e"> </span>top<span class="_ _a"> </span>10</div><div class="t m0 xe he y6c ff4 fs9 fc1 sc0 ls0 ws0">essential<span class="_ _e"> </span>nodes<span class="_ _e"> </span>ranked<span class="_ _e"> </span>by<span class="_ _e"> </span>MCC<span class="_ _e"> </span>scores<span class="_ _a"> </span>were<span class="_ _e"> </span>selected<span class="_ _e"> </span>(control<span class="_ _e"> </span>panel<span class="_ _e"> </span>|<span class="_ _a"> </span>hubba<span class="_ _e"> </span>|<span class="_ _e"> </span><span class="ffd">&#174;<span class="_ _a"> </span></span>select<span class="_ _e"> </span>nodes<span class="ffd">&#174;<span class="_ _e"> </span></span>make<span class="_ _e"> </span>check<span class="_ _e"> </span>on<span class="_ _a"> </span><span class="ff5">&#8220;</span>hubba<span class="_ _e"> </span>nodes"<span class="ffd">&#174;<span class="_ _e"> </span></span>select<span class="_ _e"> </span>a</div><div class="t m0 xe he y6d ff4 fs9 fc1 sc0 ls0 ws0">method<span class="_ _e"> </span>from<span class="_ _e"> </span><span class="ff5">&#8220;</span>choose<span class="_ _e"> </span>a<span class="_ _e"> </span>ranking<span class="_ _e"> </span>method<span class="ff5">&#8221;<span class="_ _a"> </span></span>and<span class="_ _e"> </span>determine<span class="_ _e"> </span>how<span class="_ _e"> </span>many<span class="_ _e"> </span>nodes<span class="_ _a"> </span>are<span class="_ _e"> </span>selected<span class="_ _e"> </span>from<span class="_ _e"> </span><span class="ff5">&#8220;</span>top<span class="_ _e"> </span>group<span class="ff5">&#8221;<span class="_ _a"> </span><span class="ffd">&#174;<span class="_ _e"> </span></span></span>[submit])from<span class="_ _e"> </span>the<span class="_ _e"> </span>yeast<span class="_ _e"> </span>network.</div><div class="t m0 xe he y6e ff4 fs9 fc1 sc0 ls0 ws0">(B)<span class="_ _e"> </span>Node<span class="_ _e"> </span>and<span class="_ _e"> </span>edge<span class="_ _e"> </span>annotations<span class="_ _e"> </span>are<span class="_ _a"> </span>accessible<span class="_ _e"> </span>through<span class="_ _e"> </span>Cytoscape<span class="_ _e"> </span>Data<span class="_ _e"> </span>Panel.</div><div class="t m0 x2 hb y6f ff3 fs9 fc1 sc0 ls0 ws0">Chin<span class="_ _e"> </span><span class="ff2">et<span class="_ _e"> </span>al</span>.<span class="_ _e"> </span><span class="ff2">BMC<span class="_ _a"> </span>Systems<span class="_ _e"> </span>Biology<span class="_ _e"> </span></span>2014,<span class="_ _e"> </span><span class="ff1">8</span>(Suppl<span class="_ _e"> </span>4):S11</div><div class="t m0 x2 hb y70 ff3 fs9 fc1 sc0 ls0 ws0">http://www.biomedcentral.com/1752-0509/8/S4/S<span class="_ _9"></span>11</div><div class="t m0 x13 hb y6f ff3 fs9 fc1 sc0 ls0 ws0">Page<span class="_ _e"> </span>2<span class="_ _e"> </span>of<span class="_ _e"> </span>7</div><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a></div><div class="pi" data-data='{"ctm":[1.612697,0.000000,0.000000,1.612697,0.000000,0.000000]}'></div></div><div id="pf3" class="pf w0 h0" data-page-no="3"><div class="pc pc3 w0 h0"><img class="bi x0 y0 w1 h1" alt="" src="/image.php?url=https://csdnimg.cn/release/download_crawler_static/89620325/bg3.jpg"><div class="t m0 x2 h8 y41 ff8 fs6 fc1 sc0 ls3f ws0">direct<span class="_ _6"> </span>link<span class="_ _5"> </span>in<span class="_ _6"> </span>between,<span class="_ _6"> </span><span class="ff9 ls40">cyt<span class="_"> </span>oHubba<span class="_ _6"> </span></span><span class="ls41">provides<span class="_ _5"> </span>a<span class="_ _6"> </span>shortest</span></div><div class="t m0 x2 h8 y42 ff8 fs6 fc1 sc0 ls42 ws0">path<span class="_ _6"> </span>detect<span class="_"> </span>ion<span class="_ _6"> </span>tool<span class="_ _5"> </span>(<span class="ffc ls0">&#8220;<span class="_ _7"></span><span class="ff9 ls43">display<span class="_ _6"> </span>the<span class="_ _6"> </span>shortest<span class="_ _5"> </span>path</span><span class="ffa">&#8221;<span class="_ _5"> </span></span></span><span class="ls44">on<span class="_ _6"> </span>the</span></div><div class="t m0 x2 h8 y43 ff8 fs6 fc1 sc0 ls0 ws0">display<span class="_ _8"> </span>option).<span class="_ _6"> </span>All<span class="_ _6"> </span>connectible<span class="_ _6"> </span>but<span class="_ _6"> </span>not<span class="_ _6"> </span>direct<span class="_ _6"> </span>connected</div><div class="t m0 x2 h8 y44 ff8 fs6 fc1 sc0 ls0 ws0">node<span class="_ _8"> </span>pairs<span class="_ _6"> </span>in<span class="_ _6"> </span>a<span class="_ _8"> </span>network,<span class="_ _6"> </span>retrieved<span class="_ _6"> </span>either<span class="_ _8"> </span>by<span class="_ _6"> </span>ID<span class="_ _6"> </span>search<span class="_ _6"> </span>or</div><div class="t m0 x2 h8 y45 ff8 fs6 fc1 sc0 ls45 ws0">by<span class="_ _5"> </span>top-ranked<span class="_ _5"> </span>in<span class="_ _5"> </span>to<span class="_"> </span>pological<span class="_ _5"> </span>feature<span class="_ _5"> </span>score,<span class="_ _5"> </span>ar<span class="_"> </span>e<span class="_ _6"> </span>con-</div><div class="t m0 x2 h8 y46 ff8 fs6 fc1 sc0 ls0 ws0">nected<span class="_ _6"> </span>by<span class="_ _6"> </span>dotted-li<span class="_ _7"></span>nes<span class="_ _6"> </span>with<span class="_ _6"> </span>number<span class="_ _6"> </span>of<span class="_ _6"> </span>the<span class="_ _6"> </span>smallest<span class="_ _6"> </span>ed<span class="_ _7"></span>ge</div><div class="t m0 x2 h8 y47 ff8 fs6 fc1 sc0 ls0 ws0">numbe<span class="_ _7"></span>r<span class="_ _6"> </span>(shor<span class="_ _7"></span>test<span class="_ _6"> </span>pat<span class="_ _7"></span>h)<span class="_ _6"> </span>to<span class="_ _6"> </span>ma<span class="_ _7"></span>ke<span class="_ _6"> </span>thi<span class="_"> </span>s<span class="_ _6"> </span>l<span class="_ _7"></span>ink.<span class="_ _6"> </span>The<span class="_ _5"> </span>stepp<span class="_ _7"></span>ing-</div><div class="t m0 x2 h8 y48 ff8 fs6 fc1 sc0 ls0 ws0">stone<span class="_ _5"> </span>nodes<span class="_ _6"> </span>an<span class="_ _7"></span>d<span class="_ _6"> </span>edges<span class="_ _5"> </span>compo<span class="_ _7"></span>sing<span class="_ _6"> </span>the<span class="_ _5"> </span>short<span class="_ _7"></span>est<span class="_ _6"> </span>pat<span class="_ _7"></span>h<span class="_ _6"> </span>will</div><div class="t m0 x2 h8 y49 ff8 fs6 fc1 sc0 ls46 ws0">be<span class="_ _6"> </span>expanded<span class="_ _6"> </span>by<span class="_ _6"> </span>a<span class="_ _6"> </span>mouse<span class="_ _6"> </span>right-click<span class="_ _6"> </span>action.<span class="_ _6"> </span>Comparing</div><div class="t m0 x2 h8 y4a ff8 fs6 fc1 sc0 ls47 ws0">with<span class="_ _5"> </span>the<span class="_ _5"> </span>other<span class="_ _5"> </span>cytoscape<span class="_ _5"> </span>plugin<span class="_ _5"> </span>Short<span class="_"> </span>estPath<span class="_ _6"> </span>which</div><div class="t m0 x2 h8 y4b ff8 fs6 fc1 sc0 ls48 ws0">sketches<span class="_ _6"> </span>the<span class="_ _5"> </span>path<span class="_ _5"> </span>between<span class="_ _5"> </span>two<span class="_ _6"> </span>nodes<span class="_ _5"> </span>[5],<span class="_ _5"> </span><span class="ff9 ls49">cytoHubba</span></div><div class="t m0 x2 h8 y4c ff8 fs6 fc1 sc0 ls4a ws0">fetches<span class="_ _6"> </span>the<span class="_ _8"> </span>s<span class="_"> </span>hortes<span class="_"> </span>t<span class="_ _6"> </span>path<span class="_ _6"> </span>among<span class="_ _6"> </span>a<span class="_ _6"> </span>group<span class="_ _6"> </span>of<span class="_ _6"> </span>nodes.<span class="_ _6"> </span>This</div><div class="t m0 x2 h8 y71 ff8 fs6 fc1 sc0 ls4b ws0">abstractive<span class="_ _6"> </span>view<span class="_ _6"> </span>provides<span class="_ _6"> </span>the<span class="_ _6"> </span>distance<span class="_ _6"> </span>among<span class="_ _6"> </span>essential</div><div class="t m0 x2 h8 y72 ff8 fs6 fc1 sc0 ls0 ws0">nodes.</div><div class="t m0 x2 hd y4f ff7 fsb fc1 sc0 ls0 ws0">The<span class="_ _a"> </span>performance</div><div class="t m0 x2 h8 y73 ff8 fs6 fc1 sc0 ls4c ws0">The<span class="_ _a"> </span>studies<span class="_ _a"> </span>of<span class="_ _a"> </span>protein-protein<span class="_ _a"> </span>interactions<span class="_ _8"> </span>will<span class="_ _a"> </span>be<span class="_ _a"> </span>more</div><div class="t m0 x2 h8 y74 ff8 fs6 fc1 sc0 ls0 ws0">powerful<span class="_ _a"> </span>whe<span class="_"> </span>n<span class="_ _8"> </span>the<span class="_ _e"> </span>inte<span class="_ _7"></span>ractome<span class="_ _a"> </span>co<span class="_"> </span>vera<span class="_ _7"></span>ge<span class="_ _a"> </span>increases.<span class="_ _a"> </span>How<span class="_ _7"></span>-</div><div class="t m0 x2 h8 y75 ff8 fs6 fc1 sc0 ls4d ws0">ever,<span class="_ _a"> </span>the<span class="_ _8"> </span>complexity<span class="_ _a"> </span>of<span class="_ _8"> </span>the<span class="_ _8"> </span>network<span class="_ _a"> </span>will<span class="_ _8"> </span>also<span class="_ _a"> </span>increase,</div><div class="t m0 x2 h8 y76 ff8 fs6 fc1 sc0 ls0 ws0">that<span class="_ _e"> </span>always<span class="_ _a"> </span>hampers<span class="_ _a"> </span>computation<span class="_ _a"> </span>tasks.<span class="_ _e"> </span>After<span class="_ _a"> </span>the<span class="_ _a"> </span>optimi-</div><div class="t m0 x2 h8 y77 ff8 fs6 fc1 sc0 ls0 ws0">zation<span class="_ _e"> </span>on<span class="_ _e"> </span>the<span class="_ _a"> </span>programs,<span class="_ _e"> </span><span class="ff9">cytoHubba<span class="_ _e"> </span></span>is<span class="_ _a"> </span>able<span class="_ _e"> </span>to<span class="_ _e"> </span>complete<span class="_ _a"> </span>all</div><div class="t m0 x2 h8 y78 ff8 fs6 fc1 sc0 ls4e ws0">eleven<span class="_ _a"> </span>analysis<span class="_ _a"> </span>of<span class="_ _8"> </span>a<span class="_ _8"> </span>small<span class="_ _a"> </span>network<span class="_ _a"> </span>(e.g.<span class="_ _8"> </span>330<span class="_ _a"> </span>nodes,<span class="_ _8"> </span>360</div><div class="t m0 x2 h8 y79 ff8 fs6 fc1 sc0 ls0 ws0">edges),<span class="_ _a"> </span>a<span class="_ _a"> </span>mid<span class="_"> </span>dle<span class="_ _8"> </span>size<span class="_ _a"> </span>one<span class="_ _a"> </span>(7,6<span class="_ _7"></span>00<span class="_ _a"> </span>nodes,<span class="_ _a"> </span>20,000<span class="_ _8"> </span>edges)<span class="_ _a"> </span>and</div><div class="t m0 x2 h8 y7a ff8 fs6 fc1 sc0 ls4f ws0">a<span class="_ _a"> </span>large<span class="_ _a"> </span>set<span class="_ _8"> </span>(11,500<span class="_ _a"> </span>nodes,<span class="_ _8"> </span>33,600<span class="_ _a"> </span>edges)<span class="_ _8"> </span>in<span class="_ _a"> </span>few<span class="_ _8"> </span>seconds,</div><div class="t m0 x2 h8 y7b ff8 fs6 fc1 sc0 ls50 ws0">around<span class="_ _8"> </span>30<span class="_ _a"> </span>seco<span class="_"> </span>nds<span class="_ _a"> </span>a<span class="_"> </span>nd<span class="_ _a"> </span>fe<span class="_"> </span>w<span class="_ _a"> </span>minute<span class="_"> </span>s,<span class="_ _a"> </span>respe<span class="_"> </span>ctively,<span class="_ _8"> </span>on<span class="_ _a"> </span>a</div><div class="t m0 x2 h8 y7c ff8 fs6 fc1 sc0 ls51 ws0">common<span class="_ _a"> </span>desktop/<span class="_ _a"> </span>notebook<span class="_ _8"> </span>(Cytoscape<span class="_ _a"> </span>version<span class="_ _8"> </span>2.6.x<span class="_ _a"> </span>/</div><div class="t m0 x2 h8 y7d ff8 fs6 fc1 sc0 ls52 ws0">2.7.x<span class="_ _a"> </span>/<span class="_ _a"> </span>2.8.x<span class="_ _8"> </span>on<span class="_ _a"> </span>Window<span class="_ _8"> </span>7/8<span class="_ _a"> </span>platform;<span class="_ _a"> </span>hardware<span class="_ _8"> </span>spec<span class="_ _a"> </span>as</div><div class="t m0 x2 h8 y7e ff8 fs6 fc1 sc0 ls53 ws0">Intel<span class="_ _8"> </span>i7,<span class="_ _8"> </span>8<span class="_ _a"> </span>GB<span class="_ _8"> </span>of<span class="_ _8"> </span>RAM).<span class="_ _8"> </span><span class="ff9 ls54">CytoHubba<span class="_ _8"> </span></span><span class="ls55">has<span class="_ _8"> </span>been<span class="_ _a"> </span>updated</span></div><div class="t m0 x2 h8 y7f ff8 fs6 fc1 sc0 ls56 ws0">several<span class="_ _a"> </span>times<span class="_ _8"> </span>since<span class="_ _a"> </span>2009<span class="_ _8"> </span>(from<span class="_ _a"> </span>v1.0<span class="_ _8"> </span>to<span class="_ _8"> </span>v1.6).<span class="_ _a"> </span>It<span class="_ _a"> </span>is<span class="_ _8"> </span>freely</div><div class="t m0 x2 h8 y80 ff8 fs6 fc1 sc0 ls0 ws0">access<span class="_ _7"></span>ible<span class="_ _8"> </span>in<span class="_ _a"> </span>Cyt<span class="_"> </span>o<span class="_ _7"></span>scap<span class="_ _7"></span>e<span class="_ _a"> </span>App<span class="_ _a"> </span>st<span class="_ _7"></span>ore<span class="_ _a"> </span>(ht<span class="_ _7"></span>tp:/<span class="_ _7"></span>/apps<span class="_ _7"></span>.cyt<span class="_"> </span>os<span class="_ _7"></span>cape<span class="_ _7"></span>.</div><div class="t m0 x2 h8 y81 ff8 fs6 fc1 sc0 ls57 ws0">org/apps/cytohubba).<span class="_ _8"> </span>The<span class="_ _8"> </span>accumul<span class="_"> </span>ated<span class="_ _a"> </span>dow<span class="_"> </span>nloading</div><div class="t m0 x2 h8 y82 ff8 fs6 fc1 sc0 ls58 ws0">number<span class="_ _a"> </span>is<span class="_ _8"> </span>around<span class="_ _a"> </span>6,500<span class="_ _8"> </span>(http://chianti.ucsd.edu/cyto_-</div><div class="t m0 x2 h8 y83 ff8 fs6 fc1 sc0 ls59 ws0">web/plugins/plugindownloadstatistics.php,<span class="_ _a"> </span>statistics<span class="_ _8"> </span>on</div><div class="t m0 x2 h8 y84 ff8 fs6 fc1 sc0 ls0 ws0">May<span class="_ _a"> </span>2014).<span class="_ _8"> </span>And<span class="_ _a"> </span>it<span class="_ _a"> </span>is<span class="_ _a"> </span>used<span class="_ _a"> </span>wid<span class="_ _7"></span>ely<span class="_ _a"> </span>to<span class="_ _a"> </span>anal<span class="_ _7"></span>yze<span class="_ _a"> </span>cancer<span class="_ _a"> </span>meta<span class="_ _7"></span>-</div><div class="t m0 x2 h8 y85 ff8 fs6 fc1 sc0 ls5a ws0">bolic<span class="_ _a"> </span>network[6],<span class="_ _8"> </span>innate<span class="_ _8"> </span>immune<span class="_ _a"> </span>network[7],<span class="_ _8"> </span>complex</div><div class="t m0 x2 h8 y86 ff8 fs6 fc1 sc0 ls5b ws0">biofilm<span class="_ _e"> </span>communities[8]<span class="_ _a"> </span>and<span class="_ _a"> </span>so<span class="_ _e"> </span>on.</div><div class="t m0 x2 hd y87 ff7 fsb fc1 sc0 ls0 ws0">Validation<span class="_ _a"> </span>by<span class="_ _8"> </span>Predict<span class="_ _8"> </span>yeast<span class="_ _8"> </span>essential<span class="_ _8"> </span>proteins</div><div class="t m0 x2 h8 y88 ff8 fs6 fc1 sc0 ls0 ws0">We<span class="_ _a"> </span>u<span class="_ _7"></span>se<span class="_ _a"> </span><span class="ff9 ls2">cytoHubba<span class="_ _a"> </span></span>to<span class="_ _8"> </span>scor<span class="_ _7"></span>e<span class="_ _a"> </span>al<span class="_ _7"></span>l<span class="_ _a"> </span>pro<span class="_ _7"></span>tei<span class="_ _7"></span>ns<span class="_ _a"> </span>i<span class="_ _7"></span>n<span class="_ _a"> </span>th<span class="_ _7"></span>e<span class="_ _a"> </span>yea<span class="_ _7"></span>st<span class="_ _8"> </span>pro<span class="_"> </span>-</div><div class="t m0 x2 h8 y89 ff8 fs6 fc1 sc0 ls5c ws0">tein<span class="_ _8"> </span>interaction<span class="_ _8"> </span>network<span class="_ _8"> </span>by<span class="_ _8"> </span>the<span class="_ _8"> </span>e<span class="_"> </span>leven<span class="_ _a"> </span>methods.<span class="_ _8"> </span>DIP</div><div class="t m0 x2 h8 y8a ff8 fs6 fc1 sc0 ls5b ws0">database<span class="_ _a"> </span>(ht<span class="_ _7"></span>tp://dip.do<span class="_"> </span>e-mbi<span class="_ _7"></span>.ucla.<span class="_ _7"></span>edu,<span class="_ _a"> </span>version:<span class="_ _a"> </span>201<span class="_ _7"></span>40117)</div><div class="t m0 x2 h8 y8b ff8 fs6 fc1 sc0 ls5d ws0">is<span class="_ _a"> </span>composed<span class="_ _8"> </span>of<span class="_ _8"> </span>4,908<span class="_ _8"> </span>proteins<span class="_ _a"> </span>and<span class="_ _8"> </span>21,732<span class="_ _8"> </span>interactions</div><div class="t m0 x2 h8 y8c ff8 fs6 fc1 sc0 ls5e ws0">after<span class="_ _a"> </span>removing<span class="_ _8"> </span>self-interactions<span class="_ _a"> </span>and<span class="_ _a"> </span>redundant<span class="_ _8"> </span>records.</div><div class="t m0 x2 h8 y8d ff8 fs6 fc1 sc0 ls5f ws0">The<span class="_ _a"> </span>essential<span class="_ _8"> </span>protein<span class="_ _a"> </span>lists<span class="_ _8"> </span>are<span class="_ _a"> </span>collected<span class="_ _8"> </span>from<span class="_ _a"> </span><span class="ff9 ls18">Saccharo-</span></div><div class="t m0 x2 h8 y8e ff9 fs6 fc1 sc0 ls7 ws0">myces<span class="_ _a"> </span><span class="ff8 ls60">Genome<span class="_ _8"> </span>Deletion<span class="_ _a"> </span>Project<span class="_ _8"> </span>(SGDP)<span class="_ _a"> </span>and<span class="_ _8"> </span></span><span class="ls4b">Saccharo-</span></div><div class="t m0 x2 h8 y8f ff9 fs6 fc1 sc0 ls61 ws0">myces<span class="_ _8"> </span><span class="ff8 ls62">Genome<span class="_ _8"> </span>Databa<span class="_"> </span>se<span class="_ _8"> </span>(SGD).<span class="_ _8"> </span>There<span class="_ _8"> </span>are<span class="_ _8"> </span>1,122<span class="_ _6"> </span>and</span></div><div class="t m0 x2 h8 y90 ff8 fs6 fc1 sc0 ls0 ws0">1,280<span class="_ _a"> </span>pr<span class="_ _7"></span>oteins<span class="_ _a"> </span>de<span class="_ _7"></span>fined<span class="_ _8"> </span>as<span class="_ _a"> </span>essent<span class="_ _7"></span>ial<span class="_ _a"> </span>pr<span class="_"> </span>ote<span class="_ _7"></span>ins<span class="_ _a"> </span>by<span class="_ _8"> </span>SGDP<span class="_ _a"> </span>and</div><div class="t m0 x2 h8 y91 ff8 fs6 fc1 sc0 ls63 ws0">SGD<span class="_ _a"> </span>respectively.<span class="_ _a"> </span>We<span class="_ _a"> </span>use<span class="_ _8"> </span>the<span class="_ _a"> </span>union<span class="_ _a"> </span>set<span class="_ _a"> </span>(1,297<span class="_ _8"> </span>proteins)</div><div class="t m0 x2 h8 y92 ff8 fs6 fc1 sc0 ls0 ws0">for<span class="_ _e"> </span>verifying<span class="_ _a"> </span>the<span class="_ _a"> </span>performance<span class="_ _a"> </span>of<span class="_ _e"> </span>the<span class="_ _a"> </span>predictions.</div><div class="t m0 x14 h8 y93 ff8 fs6 fc1 sc0 ls0 ws0">The<span class="_ _f"> </span>stati<span class="_ _9"></span>sti<span class="_ _9"></span>cs<span class="_ _f"> </span>of<span class="_ _f"> </span>yeast<span class="_ _f"> </span>PPIs<span class="_ _f"> </span>are<span class="_ _f"> </span>shown<span class="_ _f"> </span>in<span class="_ _e"> </span>Tabl<span class="_ _9"></span>e<span class="_ _f"> </span>1.<span class="_ _e"> </span>Twe<span class="_ _9"></span>nty</div><div class="t m0 x2 h8 y94 ff8 fs6 fc1 sc0 ls0 ws0">three<span class="_ _f"> </span>percen<span class="_ _9"></span>t<span class="_ _f"> </span>(=1148/4<span class="_ _9"></span>908)<span class="_ _f"> </span>of<span class="_ _e"> </span>the<span class="_ _e"> </span>prot<span class="_ _9"></span>eins<span class="_ _f"> </span>in<span class="_ _e"> </span>this<span class="_ _f"> </span>network</div><div class="t m0 x2 h8 y95 ff8 fs6 fc1 sc0 ls0 ws0">are<span class="_ _8"> </span>def<span class="_ _7"></span>ined<span class="_ _8"> </span>as<span class="_ _a"> </span>es<span class="_ _7"></span>se<span class="_"> </span>n<span class="_ _7"></span>tia<span class="_ _7"></span>l<span class="_ _a"> </span>pr<span class="_ _7"></span>ote<span class="_ _7"></span>ins<span class="_ _8"> </span>in<span class="_ _a"> </span>th<span class="_ _7"></span>e<span class="_ _a"> </span>da<span class="_ _7"></span>tas<span class="_ _7"></span>et.<span class="_ _8"> </span>We<span class="_ _a"> </span>c<span class="_ _7"></span>all<span class="_ _a"> </span>a</div><div class="t m0 x2 h8 y96 ff8 fs6 fc1 sc0 ls64 ws0">n<span class="_ _c"></span>o<span class="_ _11"></span>d<span class="_ _c"></span>ei<span class="_ _c"></span>sh<span class="_ _11"></span>i<span class="_ _c"></span>g<span class="_ _11"></span>h<span class="_ _b"></span>-<span class="_ _11"></span>d<span class="_ _c"></span>e<span class="_ _11"></span>g<span class="_ _c"></span>r<span class="_ _c"></span>e<span class="_ _11"></span>ei<span class="_ _c"></span>ft<span class="_ _11"></span>h<span class="_ _b"></span>e<span class="_ _7"></span>n<span class="_ _c"></span>u<span class="_ _11"></span>m<span class="_ _c"></span>b<span class="_ _c"></span>e<span class="_ _11"></span>ro<span class="_ _c"></span>fi<span class="_ _11"></span>t<span class="_ _b"></span>sn<span class="_ _11"></span>e<span class="_ _c"></span>i<span class="_ _11"></span>g<span class="_ _b"></span>h<span class="_ _11"></span>b<span class="_ _c"></span>o<span class="_ _11"></span>r<span class="_ _c"></span>si<span class="_ _c"></span>sg<span class="_ _11"></span>r<span class="_ _c"></span>e<span class="_ _11"></span>a<span class="_ _b"></span>t<span class="_ _11"></span>e<span class="_ _c"></span>r</div><div class="t m0 x2 h8 y97 ff8 fs6 fc1 sc0 ls65 ws0">than<span class="_ _a"> </span>a<span class="_ _e"> </span>threshold;<span class="_ _a"> </span>otherwise<span class="_ _a"> </span>we<span class="_ _a"> </span>call<span class="_ _a"> </span>it<span class="_ _e"> </span>a<span class="_ _a"> </span>low-degree<span class="_ _a"> </span>node,</div><div class="t m0 xf h8 y98 ff8 fs6 fc1 sc0 ls66 ws0">where<span class="_ _a"> </span>the<span class="_ _8"> </span>threshold<span class="_ _a"> </span>is<span class="_ _8"> </span>the<span class="_ _a"> </span>maximum<span class="_ _8"> </span>integer<span class="_ _a"> </span>such<span class="_ _8"> </span>that</div><div class="t m0 xf hf y99 ffe fsc fc1 sc0 ls0 ws0">2<span class="_ _f"> </span><span class="fff">&#215;</span></div><div class="c xf y9a w2 h10"><div class="t m0 x15 h11 y9b ff10 fsc fc1 sc0 ls0 ws0"><span class="fc2 sc0">&#58882;</span></div></div><div class="t m0 x16 h12 y9c ff11 fsa fc1 sc0 ls0 ws0">v<span class="fff">&#8712;</span>V<span class="_ _12"></span><span class="ffe">,</span><span class="ls67">De</span></div><div class="c xf y9a w2 h10"><div class="t m0 x17 h13 y9d ff11 fsa fc1 sc0 ls0 ws0">g</div></div><div class="t m0 x18 h13 y9c ff12 fsa fc1 sc0 ls0 ws0">(<span class="ff11">v</span><span class="ls68">)&gt;</span><span class="ff11">t</span></div><div class="t m0 x19 hf y99 ff11 fsc fc1 sc0 ls69 ws0">Deg<span class="ffe ls0">(<span class="ff11">v</span>)<span class="_ _a"> </span><span class="ff12">&gt;</span></span></div><div class="c xf y9a w2 h10"><div class="t m0 x1a h11 y9b ff10 fsc fc1 sc0 ls0 ws0"><span class="fc2 sc0">&#58882;</span></div></div><div class="t m0 x1b h13 y9c ff11 fsa fc1 sc0 ls0 ws0">v<span class="fff">&#8712;</span>V</div><div class="t m0 x1c hf y99 ff11 fsc fc1 sc0 ls69 ws0">Deg<span class="ffe ls0">(<span class="ff11">v</span></span></div><div class="c xf y9a w2 h10"><div class="t m0 x1d hf y9e ffe fsc fc1 sc0 ls0 ws0">)</div></div><div class="t m0 x1e h8 y9f ff8 fs6 fc1 sc0 ls6a ws0">.T<span class="_ _b"></span>h<span class="_ _b"></span>et<span class="_ _b"></span>h<span class="_ _c"></span>r<span class="_ _b"></span>e<span class="_ _b"></span>s<span class="_ _b"></span>h<span class="_ _c"></span>o<span class="_ _b"></span>l<span class="_ _b"></span>d</div><div class="t m0 xf h8 ya0 ff8 fs6 fc1 sc0 ls6b ws0">of<span class="_ _e"> </span>the<span class="_ _e"> </span>PPI<span class="_ _e"> </span>network<span class="_ _e"> </span>(DIP<span class="_ _e"> </span>20140117)<span class="_ _e"> </span>used<span class="_ _e"> </span>in<span class="_ _e"> </span>this<span class="_ _e"> </span>paper<span class="_ _e"> </span>is<span class="_ _e"> </span>21.</div><div class="t m0 xf h8 ya1 ff8 fs6 fc1 sc0 ls6c ws0">As<span class="_ _e"> </span>shown<span class="_ _f"> </span>as<span class="_ _e"> </span>Tabl<span class="_ _7"></span>e<span class="_ _f"> </span>1,<span class="_ _e"> </span>there<span class="_ _e"> </span>are<span class="_ _e"> </span>4,396<span class="_ _e"> </span>proteins<span class="_ _e"> </span>in<span class="_ _e"> </span>low-degree</div><div class="t m0 xf h8 ya2 ff8 fs6 fc1 sc0 ls6d ws0">category<span class="_ _f"> </span>and<span class="_ _e"> </span>512<span class="_ _f"> </span>proteins<span class="_ _e"> </span>in<span class="_ _e"> </span>high-degree<span class="_ _f"> </span>category,<span class="_ _e"> </span>in<span class="_ _e"> </span>which</div><div class="t m0 xf h8 ya3 ff8 fs6 fc1 sc0 ls6e ws0">9<span class="_ _c"></span>0<span class="_ _11"></span>8p<span class="_ _c"></span>r<span class="_ _c"></span>o<span class="_ _11"></span>t<span class="_ _c"></span>e<span class="_ _11"></span>i<span class="_ _b"></span>n<span class="_ _11"></span>sa<span class="_ _c"></span>n<span class="_ _11"></span>d2<span class="_ _b"></span>1<span class="_ _11"></span>4p<span class="_ _c"></span>r<span class="_ _11"></span>o<span class="_ _b"></span>t<span class="_ _11"></span>e<span class="_ _c"></span>i<span class="_ _11"></span>n<span class="_ _c"></span><span class="ls6f">s<span class="_ _f"> </span>are<span class="_ _e"> </span>essential<span class="_ _e"> </span>protei<span class="_ _7"></span>ns.</span></div><div class="t m0 x10 h8 ya4 ff8 fs6 fc1 sc0 ls37 ws0">Table<span class="_ _6"> </span>2<span class="_ _6"> </span>shows<span class="_ _6"> </span>the<span class="_ _5"> </span>performance<span class="_ _6"> </span>(precision<span class="_ _6"> </span>of<span class="_ _6"> </span>predic-</div><div class="t m0 xf h8 ya5 ff8 fs6 fc1 sc0 ls70 ws0">tion)<span class="_ _6"> </span>to<span class="_ _6"> </span>predict<span class="_ _8"> </span>essential<span class="_ _6"> </span>proteins<span class="_ _6"> </span>in<span class="_ _6"> </span>top<span class="_ _6"> </span>&#215;<span class="_ _6"> </span>ranked<span class="_ _6"> </span>node</div><div class="t m0 xf h8 ya6 ff8 fs6 fc1 sc0 ls70 ws0">identified<span class="_ _8"> </span>by<span class="_ _6"> </span>each<span class="_ _6"> </span>method.<span class="_ _5"> </span>In<span class="_ _8"> </span>most<span class="_ _6"> </span>methods,<span class="_ _6"> </span>the<span class="_ _6"> </span>preci-</div><div class="t m0 xf h8 ya7 ff8 fs6 fc1 sc0 ls71 ws0">sion<span class="_ _d"> </span>decrea<span class="_"> </span>ses<span class="_ _5"> </span>w<span class="_"> </span>hen<span class="_ _d"> </span>the<span class="_ _d"> </span>selected<span class="_ _d"> </span>n<span class="_"> </span>umber<span class="_ _d"> </span>increase.</div><div class="t m0 xf h8 ya8 ff8 fs6 fc1 sc0 ls72 ws0">Besides,<span class="_ _6"> </span>a<span class="_ _d"> </span>local-based<span class="_ _6"> </span>method<span class="_ _5"> </span>is<span class="_ _5"> </span>better<span class="_ _5"> </span>than<span class="_ _5"> </span>global-</div><div class="t m0 xf h8 ya9 ff8 fs6 fc1 sc0 ls0 ws0">based<span class="_ _6"> </span>meth<span class="_ _7"></span>od<span class="_ _8"> </span>i<span class="_ _7"></span>n<span class="_ _8"> </span>dis<span class="_ _7"></span>covering<span class="_ _6"> </span>yea<span class="_ _7"></span>st<span class="_ _6"> </span>essenti<span class="_ _7"></span>al<span class="_ _8"> </span>pro<span class="_ _7"></span>teins.<span class="_ _6"> </span>To</div><div class="t m0 xf h8 yaa ff8 fs6 fc1 sc0 ls73 ws0">further<span class="_ _6"> </span>understand<span class="_ _6"> </span>the<span class="_ _6"> </span>preference<span class="_ _6"> </span>of<span class="_ _5"> </span>network<span class="_ _6"> </span>feature</div><div class="t m0 xf h8 yab ff8 fs6 fc1 sc0 ls20 ws0">selected<span class="_ _6"> </span>by<span class="_ _6"> </span>different<span class="_ _6"> </span>methods,<span class="_ _6"> </span>we<span class="_ _6"> </span>compare<span class="_ _6"> </span>the<span class="_ _6"> </span>number</div><div class="t m0 xf h8 yac ff8 fs6 fc1 sc0 ls74 ws0">of<span class="_ _6"> </span>proteins<span class="_ _5"> </span>in<span class="_ _5"> </span>common<span class="_ _6"> </span>in<span class="_ _5"> </span>the<span class="_ _5"> </span>top<span class="_ _6"> </span>100<span class="_ _5"> </span>ranked<span class="_ _5"> </span>of<span class="_ _5"> </span>any</div><div class="t m0 xf h8 yad ff8 fs6 fc1 sc0 ls4a ws0">two<span class="_ _8"> </span>scoring<span class="_ _6"> </span>methods<span class="_ _6"> </span>(Table<span class="_ _6"> </span>3).<span class="_ _8"> </span>The<span class="_ _6"> </span>top<span class="_ _6"> </span>100<span class="_ _6"> </span>ranked<span class="_ _6"> </span>list</div><div class="t m0 xf h8 yae ff8 fs6 fc1 sc0 ls75 ws0">of<span class="_ _6"> </span>Closeness<span class="_ _6"> </span>is<span class="_ _6"> </span>most<span class="_ _6"> </span>identical<span class="_ _6"> </span>to<span class="_ _6"> </span>the<span class="_ _6"> </span>result<span class="_ _5"> </span>of<span class="_ _6"> </span>Radiality</div><div class="t m0 xf h8 yaf ff8 fs6 fc1 sc0 ls76 ws0">(99%),<span class="_ _6"> </span>indicate<span class="_ _5"> </span>that<span class="_ _5"> </span>the<span class="_ _6"> </span>network<span class="_ _5"> </span>features<span class="_ _6"> </span>detected<span class="_ _5"> </span>by</div><div class="t m0 xf h8 yb0 ff8 fs6 fc1 sc0 ls76 ws0">these<span class="_ _6"> </span>two<span class="_ _5"> </span>methods<span class="_ _6"> </span>are<span class="_ _5"> </span>very<span class="_ _5"> </span><span class="ls48">similar.<span class="_ _6"> </span>MCC<span class="_ _6"> </span>shares<span class="_ _6"> </span>less</span></div><div class="t m0 xf h8 yb1 ff8 fs6 fc1 sc0 ls0 ws0">commo<span class="_ _7"></span>n<span class="_ _8"> </span>co<span class="_ _7"></span>mponen<span class="_ _7"></span>ts<span class="_ _6"> </span>to<span class="_ _6"> </span>oth<span class="_"> </span>er<span class="_ _5"> </span>metho<span class="_ _7"></span>ds<span class="_ _6"> </span>(less<span class="_ _6"> </span>th<span class="_ _7"></span>an<span class="_ _6"> </span>30%).</div><div class="t m0 xf h8 yb2 ff8 fs6 fc1 sc0 ls77 ws0">The<span class="_ _6"> </span>top<span class="_ _5"> </span>100<span class="_ _6"> </span>ranked<span class="_ _5"> </span>proteins<span class="_ _6"> </span>suggested<span class="_ _6"> </span>by<span class="_ _5"> </span>DMNC<span class="_ _6"> </span>do</div><div class="t m0 xf h8 yb3 ff8 fs6 fc1 sc0 ls78 ws0">not<span class="_ _6"> </span>appear<span class="_ _5"> </span>in<span class="_ _6"> </span>other<span class="_ _5"> </span>methods<span class="ffa ls0">&#8217;<span class="_ _5"> </span></span><span class="ls79">list<span class="_ _5"> </span>except<span class="_ _6"> </span>MCC<span class="_ _6"> </span>(30%),</span></div><div class="t m0 xf h8 yb4 ff8 fs6 fc1 sc0 ls7a ws0">means<span class="_ _6"> </span>this<span class="_ _5"> </span>method<span class="_ _6"> </span>detect<span class="_ _5"> </span>different<span class="_ _6"> </span>features<span class="_ _5"> </span>from<span class="_ _5"> </span>the</div><div class="t m0 xf h8 yb5 ff8 fs6 fc1 sc0 ls0 ws0">other<span class="_ _8"> </span>ten<span class="_ _6"> </span>methods.</div><div class="t m0 x10 h8 yb6 ff8 fs6 fc1 sc0 ls26 ws0">As<span class="_ _6"> </span>shown<span class="_ _6"> </span>as<span class="_ _5"> </span>Table<span class="_ _6"> </span>1,<span class="_ _5"> </span>in<span class="_ _6"> </span>the<span class="_ _6"> </span>y<span class="_"> </span>east<span class="_ _6"> </span>PPIs,<span class="_ _5"> </span>21%<span class="_ _6"> </span>of<span class="_ _5"> </span>pro-</div><div class="t m0 xf h8 yb7 ff8 fs6 fc1 sc0 ls4f ws0">teins<span class="_ _6"> </span>in<span class="_ _6"> </span>low<span class="_"> </span>-degree<span class="_ _6"> </span>cat<span class="_"> </span>egory<span class="_ _6"> </span>are<span class="_ _5"> </span>essential<span class="_ _6"> </span>prote<span class="_"> </span>ins<span class="_ _6"> </span>and</div><div class="t m0 xf h8 yb8 ff8 fs6 fc1 sc0 ls7b ws0">42%<span class="_ _6"> </span>of<span class="_ _5"> </span>proteins<span class="_ _5"> </span>are<span class="_ _5"> </span>essential<span class="_ _5"> </span>proteins<span class="_ _5"> </span>in<span class="_ _6"> </span>high-degree</div><div class="t m0 xf h8 yb9 ff8 fs6 fc1 sc0 ls49 ws0">category.<span class="_ _6"> </span>Accordingly,<span class="_ _5"> </span>if<span class="_ _5"> </span>we<span class="_ _5"> </span>pick<span class="_ _6"> </span>a<span class="_ _5"> </span>protein<span class="_ _5"> </span>randomly</div><div class="t m0 xf h8 yba ff8 fs6 fc1 sc0 ls0 ws0">from<span class="_ _8"> </span>the<span class="_ _8"> </span>high-degree<span class="_ _6"> </span>pool,<span class="_ _6"> </span>the<span class="_ _8"> </span>probability<span class="_ _6"> </span>that<span class="_ _8"> </span>an<span class="_ _6"> </span>essen-</div><div class="t m0 xf h8 ybb ff8 fs6 fc1 sc0 ls25 ws0">tial<span class="_ _6"> </span>protein<span class="_ _6"> </span>being<span class="_ _5"> </span>chosen<span class="_ _6"> </span>is<span class="_ _6"> </span>0.42,<span class="_ _6"> </span>an<span class="_"> </span>d<span class="_ _6"> </span>0.21<span class="_ _6"> </span>from<span class="_ _5"> </span>a<span class="_ _6"> </span>low-</div><div class="t m0 xf h8 ybc ff8 fs6 fc1 sc0 ls7c ws0">degree<span class="_ _6"> </span>protein<span class="_ _8"> </span>p<span class="_"> </span>ool<span class="_ _6"> </span>respectively.<span class="_ _6"> </span>Table<span class="_ _8"> </span>4<span class="_ _6"> </span>is<span class="_ _6"> </span>the<span class="_ _6"> </span>number</div><div class="t m0 xf h8 ybd ff8 fs6 fc1 sc0 ls7d ws0">of<span class="_ _6"> </span>essential<span class="_ _5"> </span>proteins<span class="_ _6"> </span>found<span class="_ _6"> </span>in<span class="_ _5"> </span>the<span class="_ _6"> </span>top<span class="_ _5"> </span>&#215;<span class="_ _6"> </span>list<span class="_ _6"> </span>with<span class="_ _5"> </span>low-</div><div class="t m0 xf h8 ybe ff8 fs6 fc1 sc0 ls7e ws0">degree<span class="_ _6"> </span>feature.<span class="_ _6"> </span>Fo<span class="_"> </span>r<span class="_ _6"> </span>example,<span class="_ _6"> </span>among<span class="_ _6"> </span>the<span class="_ _5"> </span>top<span class="_ _6"> </span>30<span class="_ _6"> </span>protein</div><div class="t m0 xf h8 ybf ff8 fs6 fc1 sc0 ls7f ws0">ranked<span class="_ _6"> </span>by<span class="_ _5"> </span>DMNC,<span class="_ _5"> </span>29<span class="_ _5"> </span>proteins<span class="_ _6"> </span>are<span class="_ _5"> </span>in<span class="_ _5"> </span>the<span class="_ _6"> </span>l<span class="_"> </span>ow-degree</div><div class="t m0 xf h8 yc0 ff8 fs6 fc1 sc0 ls80 ws0">category,<span class="_ _6"> </span>in<span class="_ _5"> </span>which<span class="_ _6"> </span>21<span class="_ _5"> </span>out<span class="_ _5"> </span>of<span class="_ _6"> </span>29<span class="_ _5"> </span>proteins<span class="_ _6"> </span>are<span class="_ _5"> </span>essential</div><div class="t m0 xf h8 yc1 ff8 fs6 fc1 sc0 ls81 ws0">proteins.<span class="_ _6"> </span>Methods<span class="_ _6"> </span>except<span class="_ _6"> </span>D<span class="ls75">MNC,<span class="_ _5"> </span>MCC<span class="_ _6"> </span>and<span class="_ _6"> </span>EcCentri-</span></div><div class="t m0 xf h8 yc2 ff8 fs6 fc1 sc0 ls0 ws0">city<span class="_ _8"> </span>tend<span class="_ _6"> </span>to<span class="_ _6"> </span>assign<span class="_ _6"> </span>higher<span class="_ _6"> </span>scores<span class="_ _8"> </span>to<span class="_ _6"> </span>a<span class="_ _6"> </span>node<span class="_ _8"> </span>when<span class="_ _6"> </span>it<span class="_ _6"> </span>owns</div><div class="t m0 xf h8 yc3 ff8 fs6 fc1 sc0 ls82 ws0">more<span class="_ _6"> </span>neighbors<span class="_ _5"> </span>while<span class="_ _6"> </span>almost<span class="_ _5"> </span>no<span class="_ _6"> </span>any<span class="_ _5"> </span>low-degree<span class="_ _6"> </span>pro-</div><div class="t m0 xf h8 yc4 ff8 fs6 fc1 sc0 ls83 ws0">teins<span class="_ _6"> </span>are<span class="_ _6"> </span>found<span class="_ _6"> </span>in<span class="_ _6"> </span>their<span class="_ _6"> </span>top<span class="_ _6"> </span>&#215;<span class="_ _6"> </span>list.<span class="_ _6"> </span>In<span class="_ _6"> </span>other<span class="_ _6"> </span>word,<span class="_ _6"> </span>these</div><div class="t m0 xf h8 yc5 ff8 fs6 fc1 sc0 ls0 ws0">methods<span class="_ _8"> </span>cannot<span class="_ _6"> </span>find<span class="_ _8"> </span>low-degree<span class="_ _6"> </span>essential<span class="_ _6"> </span>proteins.</div><div class="t m0 xf h6 yc6 ff1 fs4 fc1 sc0 ls0 ws0">Conclusions</div><div class="t m0 xf h8 yc7 ff8 fs6 fc1 sc0 ls0 ws0">In<span class="_ _6"> </span>th<span class="_ _7"></span>is<span class="_ _6"> </span>st<span class="_ _7"></span>udy,<span class="_ _5"> </span>we<span class="_ _6"> </span>im<span class="_"> </span>p<span class="_ _7"></span>lem<span class="_ _7"></span>ent<span class="_ _6"> </span>o<span class="_"> </span>u<span class="_ _7"></span>r<span class="_ _6"> </span>ne<span class="_ _7"></span>twor<span class="_ _7"></span>k<span class="_ _6"> </span>sco<span class="_ _7"></span>ring<span class="_ _6"> </span>m<span class="_ _7"></span>eth<span class="_ _7"></span>-</div><div class="t m0 xf h8 yc8 ff8 fs6 fc1 sc0 ls84 ws0">ods,<span class="_ _6"> </span>MCC,<span class="_ _6"> </span>MNC<span class="_ _6"> </span>and<span class="_ _5"> </span>DMNC,<span class="_ _6"> </span>and<span class="_ _6"> </span>eight<span class="_ _6"> </span>other<span class="_ _5"> </span>popular</div><div class="t m0 xf h14 yc9 ff1 fsd fc1 sc0 ls0 ws0">Table<span class="_ _a"> </span>1<span class="_ _8"> </span>Statistics<span class="_ _a"> </span>of<span class="_ _8"> </span>Yeast<span class="_ _8"> </span>PPIs<span class="_ _a"> </span>used<span class="_ _8"> </span>in<span class="_ _8"> </span>this<span class="_ _a"> </span>study<span class="_ _8"> </span>(DIP</div><div class="t m0 xf h14 yca ff1 fsd fc1 sc0 ls0 ws0">database,<span class="_ _a"> </span>20140117<span class="_ _8"> </span>released<span class="_ _a"> </span>set),<span class="_ _8"> </span>in<span class="_ _8"> </span>the<span class="_ _a"> </span>aspects<span class="_ _8"> </span>of</div><div class="t m0 xf h14 ycb ff1 fsd fc1 sc0 ls0 ws0">degree<span class="_ _a"> </span>and<span class="_ _8"> </span>essentiality</div><div class="t m0 x1f he ycc ff7 fs9 fc1 sc0 ls0 ws0">Total<span class="_ _13"> </span>Low-degree<span class="_ _13"> </span>High-degree</div><div class="t m0 x20 he ycd ff4 fs9 fc1 sc0 ls0 ws0">The<span class="_ _e"> </span>number<span class="_ _e"> </span>of<span class="_ _e"> </span>proteins<span class="_ _14"> </span>4908<span class="_ _15"> </span>4396<span class="_ _16"> </span>512</div><div class="t m0 x21 he yce ff4 fs9 fc1 sc0 ls0 ws0">Essential<span class="_ _e"> </span>proteins<span class="_ _e"> </span>(%)<span class="_ _17"> </span>1148<span class="_ _18"> </span>908<span class="_ _19"> </span>214</div><div class="t m0 x1f he ycf ff4 fs9 fc1 sc0 ls0 ws0">(23%)<span class="_ _1a"> </span>(21%)<span class="_ _1b"> </span>(42%)</div><div class="t m0 x2 hb yd0 ff3 fs9 fc1 sc0 ls0 ws0">Chin<span class="_ _e"> </span><span class="ff2">et<span class="_ _e"> </span>al</span>.<span class="_ _e"> </span><span class="ff2">BMC<span class="_ _a"> </span>Systems<span class="_ _e"> </span>Biology<span class="_ _e"> </span></span>2014,<span class="_ _e"> </span><span class="ff1">8</span>(Suppl<span class="_ _e"> </span>4):S11</div><div class="t m0 x2 hb yd1 ff3 fs9 fc1 sc0 ls0 ws0">http://www.biomedcentral.com/1752-0509/8/S4/S<span class="_ _9"></span>11</div><div class="t m0 x13 hb yd0 ff3 fs9 fc1 sc0 ls0 ws0">Page<span class="_ _e"> </span>3<span class="_ _e"> </span>of<span class="_ _e"> </span>7</div><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a><a class="l"><div class="d m6"></div></a></div><div class="pi" data-data='{"ctm":[1.612697,0.000000,0.000000,1.612697,0.000000,0.000000]}'></div></div>
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