Title: To screen the effective software for analysing gene interactions from Kashin-Beck disease genome profiling pathway and network, according to the tool of GeneMANIA

Authors: Sen Wang; Weizhuo Wang; Junjie Zhao; Feng Zhang; Shulan He; Xiong Guo

Addresses: School of Public Health, Health and Science Center of Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China ' Department of Orthopedics Surgery, The Second Affiliated Hospital, Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi, China ' Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Health and Science Center of Xi'an Jiaotong University, Xi'an, Shaanxi, China ' School of Public Health, Health and Science Center of Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China ' School of Public Health, Health and Science Center of Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China ' School of Public Health, Health and Science Center of Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China

Abstract: In order to screen the more effective software for the pathway and network analysis of Kashin-Beck disease, gene microarrays, TranscriptomeBrowser, MetaCore and GeneMANIA were used for analysis. Three significant chondrocytic pathways and one network were screened by TranscriptomeBrowser; one significant pathway and one network were identified by MetaCore. BAX, APAF1, CASP6, BCL2, VEGF, SOCS3, BAK, TGFBI, TNFAIP6, TNFRSF11B and THBS1 were significant genes associated with the biological function of chondrocyte or cartilage involved in the TranscriptomeBrowser or MetaCore results. The interactions between the significant genes and their adjacent genes were searched and classified in GeneMANIA. In pathway analysis results, TranscriptomeBrowser is superior to get the interaction of pathway and co-expression compared with MetaCore; MetaCore is superior to get the interaction of physical interaction compared with TranscriptomeBrowser. In network analysis results, TranscriptomeBrowser contains more interaction message of co-localisation, MetaCore contains more interaction message of co-expression.

Keywords: KBD; Kashin-Beck disease; chondrocytic pathways; chondrocyte; bioinformatics; gene microarrays; network analysis; pathway analysis; data mining; cartilage; software; gene interactions; genome profiling; significant genes; gene expression data; osteochondropathy; bone disease.

DOI: 10.1504/IJDMB.2015.068963

International Journal of Data Mining and Bioinformatics, 2015 Vol.12 No.1, pp.100 - 114

Received: 20 Apr 2013
Accepted: 22 May 2014

Published online: 22 Apr 2015 *

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