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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

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