Consistency, comprehensiveness, and compatibility of pathway databases

Background: It is necessary to analyze microarray experiments together with biological information to make better biological inferences. We investigate the adequacy of current biological databases to address this need. Description: Our results show a low level of consistency, comprehensiveness and compatibility among three popular pathway databases (KEGG, Ingenuity and Wikipathways). The level of consistency for genes in similar pathways across databases ranges from 0% to 88%. The corresponding level of consistency for interacting genes pairs is 0%-61%. These three original sources can be assumed to be reliable in the sense that the interacting gene pairs reported in them are correct because they are curated. However, the lack of concordance between these databases suggests each source has missed out many genes and interacting gene pairs. Conclusions: Researchers will hence find it challenging to obtain consistent pathway information out of these diverse data sources. It is therefore ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong
• Keywords: Biological, BMCBI 2010, Databases, Gene Pairs