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Table 2 Gene set databases collected for enrichment analysis in human. The last column gives the version of the database, secondary source, or the date of access

From: iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

Type Subtype/Database name Ref. # Gene Sets Source & Version
Gene Ontology Biological Process (BP) [100] 15,796 Ensembl 92
Cellular Component (CC)   1916 Ensembl 92
Molecular Function (MF)   4605 Ensembl 92
KEGG KEGG [101] 327 Release 86.1
Curated Biocarta [102] 249 Whichgenes 1.5 [103]
EHMN [104] 55 GeneSetDB [89]
Panther [105] 168 1.0.4
HumanCyc [106] 240 Pathway Commons V9 [107]
INOH [108] 576 Pathway Commons V9
NetPath [109] 27 Pathway Commons V9
PID [110] 223 Pathway Commons V9
PSP [111] 327 Pathway Commons V9
Recon X [112] 2339 Pathway Commons V9
Reactome [113] 2010 V64
WikiPathways [114] 457 June 10, 2018
TF.Target CircuitsDB [115] 829 V2012
ENCODE [116] 181 V70.0
Marbach2016 [117] 628 V 1.0
RegNetwork [118] 1400 July 1, 2017
TFacts [119] 428 Feb. 2012
ITFP [120] 1926 tftargets May,2017
Neph2012 [121] 16,476 tftargets May,2017
TRED [122] 131 tftargets May,2017
TRRUST [123] 793 V2
miRNA.Targets CircuitsDB [115] 140 V. 2012
MicroCosm [124] 44 GeneSetDB
miRDB [125] 2588 V 5.0
miRTarBase [126] 2599 V 7.0
RegNetwork [118] 618 V. 2015
TargetScan [127] 219 V7.2
MSigDB.Computational Computational gene set [128] 858 MSigDB 6.1
MSigDB.Curated Literature [86] 3465 MSigDB 6.1
MSigDB.Hallmark hallmark [39] 50 MSigDB 6.1
MSigDB.Immune Immune system [129] 4872 MSigDB 6.1
MSigDB.Location Cytogenetic band [86] 326 MSigDB 6.1
MSigDB.Motif TF and miRNA Motifs [49] 836 MSigDB 6.1
MSigDB.Oncogenic Oncogenic signatures [86] 189 MSigDB 6.1
PPI BioGRID [130] 15,542 3.4.160
CORUM [131] 2178 Feb. 17, 2017
BIND [132] 3807 Pathway Commons V9
DIP [133] 2630 Pathway Commons V9
HPRD [134] 7141 Pathway Commons V9
IntAct [135] 11,991 Pathway Commons V9
Drug MATADOR [136] 266 GeneSetDB
SIDER [137] 473 GeneSetDB
STITCH [138] 4616 GeneSetDB
T3DB [139] 846 GeneSetDB
SMPDB [140] 699 Pathway Commons V9
CTD [141] 8758 Pathway Commons V9
Drugbank [142] 2563 Pathway Commons V9
Other CancerGenes [143] 23 GeneSetDB
MethCancerDB [144] 21 GeneSetDB
MethyCancer [145] 54 GeneSetDB
MPO [146] 3134 GeneSetDB
HPO [147] 6785 May, 2018
Total:    140,438