Type |
Subtype/Database name |
#GeneSets |
Source |
Gene Ontology |
Biological Process (BP) |
15796 |
Ensembl 92 |
|
Cellular Component (CC) |
1916 |
Ensembl 92 |
|
Molecular Function (MF) |
4605 |
Ensembl 92 |
KEGG |
KEGG |
327 |
Release 86.1 |
Curated |
Biocarta |
249 |
Whichgenes 1.5 |
|
GeneSetDB.EHMN |
55 |
GeneSetDB |
|
Panther |
168 |
1.0.4 |
|
HumanCyc |
240 |
pathway Commons V9 |
|
INOH |
576 |
pathway Commons V9 |
|
NetPath |
27 |
pathway Commons V9 |
|
PID |
223 |
pathway Commons V9 |
|
PSP |
327 |
pathway Commons V9 |
|
Recon X |
2339 |
pathway Commons V9 |
|
Reactome |
2010 |
V64 |
|
Wiki |
457 |
20180610 |
TF.Target |
CircuitsDB.TF |
829 |
V2012 |
|
ENCODE |
181 |
V70.0 |
|
Marbach2016 |
628 |
regulatorycircuits Release 1.0 |
|
RegNetwork.TF |
1400 |
7/1/2017 |
|
TFacts |
428 |
Feb. 2012 |
|
tftargets.ITFP |
1926 |
tftargets May,2017 |
|
tftargets.Neph2012 |
16476 |
tftargets May,2017 |
|
tftargets.TRED |
131 |
tftargets May,2017 |
|
TRRUST |
793 |
V2 |
miRNA.Targets |
CircuitsDB.miRNA |
140 |
V. 2012 |
|
GeneSetDB.MicroCosm |
44 |
GeneSetDB |
|
miRDB |
2588 |
V 5.0 |
|
miRTarBase |
2599 |
V 7.0 |
|
RegNetwork.miRNA |
618 |
V. 2015 |
|
TargetScan |
219 |
V7.2 |
MSigDB.Computational |
Computational gene sets |
858 |
MSigDB 6.1 |
MSigDB.Curated |
Literature |
3465 |
MSigDB 6.1 |
MSigDB.Hallmark |
hallmark |
50 |
MSigDB 6.1 |
MSigDB.Immune |
Immune system |
4872 |
MSigDB 6.1 |
MSigDB.Location |
Cytogenetic band |
326 |
MSigDB 6.1 |
MSigDB.Motif |
TF and miRNA Motifs |
836 |
MSigDB 6.1 |
MSigDB.Oncogenic |
Oncogenic signatures |
189 |
MSigDB 6.1 |
PPI |
BioGRID |
15542 |
3.4.160 |
|
CORUM |
2178 |
02.07.2017 |
|
BIND |
3807 |
pathway Commons V9 |
|
DIP |
2630 |
pathway Commons V9 |
|
HPRD |
7141 |
pathway Commons V9 |
|
IntAct |
11991 |
pathway Commons V9 |
Drug |
GeneSetDB.MATADOR |
266 |
GeneSetDB |
|
GeneSetDB.SIDER |
473 |
GeneSetDB |
|
GeneSetDB.STITCH |
4616 |
GeneSetDB |
|
GeneSetDB.T3DB |
846 |
GeneSetDB |
|
SMPDB |
699 |
pathway Commons V9 |
|
CTD |
8758 |
pathway Commons V9 |
|
Drugbank |
2563 |
pathway Commons V9 |
Other |
GeneSetDB.CancerGenes |
23 |
GeneSetDB |
|
GeneSetDB.MethCancerDB |
21 |
GeneSetDB |
|
GeneSetDB.MethyCancer |
54 |
GeneSetDB |
|
GeneSetDB.MPO |
3134 |
GeneSetDB |
|
HPO |
6785 |
May,2018 |
Total: |
|
140,438 |
|
|
|
|
|
Type |
Source |
#Sets |
Note |
Co-expression |
Literature |
8,742 |
Differentially expressed genes from 2526 studies |
|
MSigDB |
3,964 |
Molecular Signature Database, v.6.0 |
|
L2L |
248 |
List of lists, v.2006.2 |
|
CancerGenes* |
23 |
Cancer gene lists |
|
GeneSigDB |
494 |
Gene Signature Database, R.4 |
Gene |
GO_BP |
11,943 |
V2017.5 |
Ontology |
GO_MF |
2,932 |
|
|
GO_CC |
1,475 |
|
Curated |
Biocarta* |
176 |
Metabolic and signaling pathways |
pathways |
PANTHER |
151 |
Ontology-based pathway database, v3.4.1 |
|
WikiPathways* |
146 |
Open platform for pathway curation |
|
INOH* |
73 |
Integrating network objects with hierarchies |
|
NetPath* |
25 |
Signal transduction pathways |
Metabolic |
KEGG |
314 |
Metabolic pathways, R.82.0 |
pathways |
EHMN* |
53 |
Edinburgh human metabolic network |
|
MouseCyc |
321 |
Mouse Biochemical Pathways , v2013.7 |
Drug |
CTD* |
910 |
The Comparative Toxicogenomics Database |
related |
SIDER* |
460 |
Side Effect Resource |
|
MATADOR* |
248 |
Manually Annotated Targets and Drugs Online Resource |
|
DrugBank* |
136 |
Open data drug and target database |
|
SMPDB* |
74 |
Small Molecule Pathway Database |
miRNA |
miRDB |
1,912 |
miRNA target prediction and annotations, v 5.0 |
Target |
microRNA.org |
314 |
Predicted miRNA targets, v.R2010 |
Genes |
Grimson et al. |
179 |
Predicted miRNA targets. v.6.2 |
|
TarBase |
84 |
Experimentally validated miRNA targets, v.6.0 |
|
miRTarBase |
775 |
Experimentally validated miRNA targets, V6.1 |
|
MicroCosm |
464 |
Predicted targets |
|
PicTar |
35 |
Predicted miRNA sites, v. 2007.3 |
TF Target |
TFactS* |
101 |
Predicted TF targets |
Genes |
TRED |
99 |
Confirmed TF target genes, v.2013.7 |
|
CircuitsDB |
94 |
Mixed miRNA/TF regulation, v. 2012 |
|
TRANSFAC |
78 |
Confirmed TF binding sites, v7.0 |
Others |
Location |
341 |
Genomic location on chromosomes, v.2017 |
|
HPO* |
1,518 |
The human phenotype ontology |
|
STITCH* |
3,929 |
Interaction networks of chemicals and proteins |
|
MPO* |
2,943 |
Mammalian Phenotype Ontology |
|
T3DB* |
722 |
Database of common toxins and their targets |
|
PID* |
193 |
Pathway Interaction Database |
|
MethyCancer* |
50 |
Human DNA methylation and cancer |
|
MethCancerDB* |
19 |
Aberrant DNA methylation in human cancer |
|
Total |
46,758 |
*Secondary data from GeneSetDB |