ToppGene Suite

A one-stop portal for gene list enrichment analysis and candidate gene prioritization
based on functional annotations and protein interactions network

GO Biological Process
Annotations:
16,597
Genes:
20,213
Updated Mar 12, 2021
GO Cellular Component
Annotations:
2,054
Genes:
20,269
Updated Mar 12, 2021
GO Molecular Function
Annotations:
4,899
Genes:
19,415
Updated Mar 12, 2021
Human Phenotype
Annotations:
8,400
Genes:
4,707
Mouse Phenotype
Annotations:
10,821
Genes:
11,516
Updated Mar 11, 2021
Pathways
Annotations:
2,191
GenMAPP
67
MSigDB C2 BIOCARTA (v7.3)
1,318
PantherDB
152
Pathway Ontology
321
SMPDB
333
Genes:
10,254
Domains
Annotations:
21,899
Gene3D
861
InterPro
12,487
PROSITE
1,698
Pfam
5,698
ProDom
177
SMART
978
Genes:
18,735
Pubmed
Annotations:
945,292
Genes:
38,789
Updated Mar 12, 2021
Interactions
Annotations:
19,257
Genes:
19,258
Updated Mar 12, 2021
Cytoband
Annotations:
2,354
Genes:
34,661
TFBS
Annotations:
963
MSigDB
348
TFBS
615
Genes:
24,869
miRNA
Annotations:
10,743
MSigDB
313
MicroRNA.org
2,200
MirDB
4,632
PITA
677
TargetScan
322
miRTarbase
2,599
Genes:
72,243
Gene Families
Annotations:
940
Genes:
18,194
ToppCell Atlas
Annotations:
16,608
A Cellular Census of Human Lungs (Vieira Braga et al)
249
Airway Inflammation in Cystic Fibrosis (CF)
42
Atlas of Lymphangioleiomyomatosis (LAM)
40
Bronchoalveolar Lavage (BAL) Atlas of COVID-19 Patients (Liao et al.)
108
Bronchoalveolar Lavage (BAL) Atlas of Severe COVID-19 Patients (Grant et al.)
83
CD8+ Memory T cells (PBMC) of COVID-19 Patients
107
COVID-19 B cell and Plasma cell Atlas in PBMC and BAL
123
COVID-19 BAL Atlas
83
COVID-19 Lung Atlas
222
COVID-19 PBMC Myeloid Cell Atlas
80
COVID-19 PBMC Neutrophil Atlas
29
COVID-19 PBMC Platelet Atlas
42
COVID-19 T Cell Atlas (PBMC)
54
COVID-19 T cell Atlas (BAL)
55
COVID-19 cDC Atlas
75
Colon Immune Atlas
206
Colon Immune Atlas from Gut Cell Atlas
183
Comparison of human cortex and organoids
94
Human Adult Brain MTG
264
Human Blood Atlas
53
Human Bone Marrow Atlas
78
Human Bronchial Epithelial Cells (HBEC)
43
Human Cord Blood Atlas
61
Human Fetal Lung in Development
357
Human Hepatoblastoma Atlas
48
Human Ileal Epithelial cells from Crohn’s Disease
18
Human Ileal Immune cells from Crohn's Disease
195
Human Lung Cell Atlas (HLCA)
578
Human Lung Cells in 3 Age Groups (Wang et al.)
414
Human Metastatic Lung Adenocarcinoma (Nayoung Kim et al)
526
Human Multiple Cortical Areas SMART-seq
193
Influenza Atlas
84
Integration of 5 COVID-19 PBMC Datasets
124
Integration of Multiple Sampling Location of COVID-19 Patients
1,421
Integration of immune-mediated diseases (COVID-19 + Influenza + Sepsis + Multiple Sclerosis)
384
Mouse Adult Trachea
46
Mouse Aging Atlas- Tabula Muris Senis
4,907
Mouse Bone Marrow Niche (Baccin_2019)
68
Mouse Bone Marrow Niche (Baryawno_2019)
60
Mouse Bone Marrow Niche (Tikhonova_2019)
18
Mouse Trachea Epithelial Cells (MTECs)
49
Mouse developmental Lung
102
Multiple Sclerosis
62
PBMC Atlas of COVID-19 Patients (Arunachalam et al.)
155
PBMC Atlas of COVID-19 Patients (Guo et al.)
64
PBMC Atlas of COVID-19 Patients (Schulte-Schrepping et al.)
327
PBMC Atlas of COVID-19 and Influenza Patients (Lee et al.)
235
PBMC Atlas of COVID-19 patients (Wilk et al.)
87
Pathobiology of Pulmonary Fibrosis (Reyfman et al., 2019)
275
Resident Cell Populations in IPF and COPD
363
Respiratory Tissues from Nasal Brushing to Parenchyma
42
Rheumatoid Arthritis and Lupus Nephritis Atlas
101
SARS-CoV-2 Infected Human Cell Lines
10
Sepsis Atlas
201
TCGA OncoMap
773
Tissue Stability Cell Atlas - Lung Cells
1,359
Tissue Stability Cell Atlas - Oesophagus Cells
41
Tissue Stability Cell Atlas - Spleen Cells
63
Transcriptional and Cellular Diversity of the Human Heart
140
Upper Airway and Bronchi Atlas of COVID-19 Patients
266
mouse_P3_lung_dropseq (2716 cells)
69
scRNA-seq of ileum and lung epithelial cells in macaque.
9
Genes:
36,831
Coexpression
Annotations:
12,337
GeneSigDB
3,515
MSigDB C2: CGP Curated Gene Sets (v7.3)
3,364
MSigDB C6: Oncogenic Signatures (v7.3)
189
MSigDB C7: Immunologic Signatures (v7.3)
5,219
MSigDB H: Hallmark Gene Sets (v7.3)
50
Genes:
23,951
Coexpression Atlas
Annotations:
4,968
Body Map
65
FaceBase_RNAseq
399
FaceBase_ST1
187
Gudmap Mouse MOE430.2
1,962
Gudmap Mouse ST 1.0
675
Gudmap RNAseq
180
Human Protein Atlas
37
Immgen.org, GSE15907
510
PCBC
772
PCBC_AltAnalyze
181
Genes:
21,555
Computational Gene Set
Annotations:
858
MSigDb: C4 - CGN: Cancer Gene Neighborhood (v7.2)
427
MSigDb: C4 - CM: Cancer Modules (v7.2)
431
Genes:
10,012
Drugs
Annotations:
80,510
Broad Institute CMAP Down
6,100
Broad Institute CMAP Up
6,100
CTD
12,437
Chemical and Genetic Perturbations
3,364
Drug Bank
3,803
Stitch
48,706
Genes:
24,261
Disease
Annotations:
41,675
Clinical Variations
6,353
DisGeNET BeFree
17,993
DisGeNET Curated
11,181
GWAS
291
OMIM MedGen
5,857
Genes:
19,365
Master Gene Info File
Updated Mar 12, 2021
Build Information
ToppGene2021-Mar-29 15:59 / #31 / 639dfe36cbad55ba69e8255099537d5c2fcb9483
Settings2018-Dec-17 21:32 / #3 / 328e53bf1eecab287d45c98a7262c85e1c7a117e
Visualization2019-Jan-16 21:42 / #1 / ac0dfc7ee8d9204193d592f1d8d372626eb9621a
Utilities2020-Dec-15 17:02 / #18 / 299ab5789c3ddec336e791c36cf36252cb11a975
Session2019-01-16 21:41 / #1 / f193998539321fb9c76fdd36d75d77fae3f443ef
2021-Mar-29 15:59 / #31 / 639dfe36cbad55ba69e8255099537d5c2fcb9483 node-p3