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) | Â | 1916 | Ensembl 92 | |
Molecular Function (MF) | Â | 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: | Â | Â | 140,438 | Â |