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Table 2 Lists of # of genes and relations in integrated database

From: An integrative approach to identifying cancer chemoresistance-associated pathways

Statistics information of integrated databases    
Database Organism # of gene # of relation
PID+KEGG+TRANSFAC Homo sapiens 8173 9308
Reactome Homo sapiens 538 31240
Statistics information on each of the three databases    
Database # of TFs # of target gene parsed # of pairing regulate relation parsed
TRANSFAC 157 825 529625
Database # of pathways # of gene, protein, enzyme parsed # of relation parsed
PID + KEGG 197 18937 8880
PID 60   
KEGG 137   
  1. We integrated the PID (the date of version, July 15, 2008), KEGG (release 47.0, July 1, 2008) and TRANSFAC public databases (version 7.0), and further eliminated duplicated reactions and elements. Accordingly, 8173 genes and 9308 interactions were remained. To assess the importance of genes within each filtered pathway, we also implemented the betweenness centrality and degree centrality for each node. The degree and betweenness centrality of genes were calculated using the Reactome database [31] as a base to cross validate our experimental results. Pathways downloaded from PID and KEGG were parsed by batch processing. A gene (or protein) may be involved in several pathways, which means some genes were repeated. Therefore, the number of parsed entity (including genes, proteins, and enzymes) was 18937. Moreover, one gene may be regulated by several TFs, or one TF may regulate numerous target genes. As a result, the total number of pairing regulate relation parsed was 529625.