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:
16,930
Genes:
20,720
Updated Aug 8, 2022
GO Cellular Component
Annotations:
2,122
Genes:
20,932
Updated Aug 8, 2022
GO Molecular Function
Annotations:
5,235
Genes:
19,963
Updated Aug 8, 2022
Human Phenotype
Annotations:
10,035
Genes:
5,060
Updated Jul 19, 2022
Mouse Phenotype
Annotations:
11,088
Genes:
12,941
Updated Aug 1, 2022
Pathways
Annotations:
5,006
BioSystems: BIOCYC
314
BioSystems: KEGG
406
BioSystems: Pathway Interaction Database
186
BioSystems: REACTOME
1,860
GenMAPP
67
MSigDB C2 BIOCARTA (v7.5.1)
1,367
PantherDB
152
Pathway Ontology
321
SMPDB
333
Genes:
13,609
Domains
Annotations:
21,882
Gene3D
861
InterPro
12,478
PROSITE
1,698
Pfam
5,691
ProDom
177
SMART
977
Genes:
18,678
Pubmed
Annotations:
1,043,184
Genes:
44,761
Updated Jul 19, 2022
Interactions
Annotations:
19,895
Genes:
19,896
Updated Jul 19, 2022
Cytoband
Annotations:
2,290
Genes:
33,040
TFBS
Annotations:
1,133
MSigDB
518
TFBS
615
Genes:
26,918
miRNA
Annotations:
10,743
MSigDB
313
MicroRNA.org
2,200
MirDB
4,632
PITA
677
TargetScan
322
miRTarbase
2,599
Genes:
59,110
Gene Families
Annotations:
940
Genes:
18,084
ToppCell Atlas
Annotations:
29,905
A Cellular Census of Human Lungs (Vieira Braga et al)
249
Adult human kidney single cell transcriptional and chromatin accessibility profiling
190
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 Autopsy Atlas (Lung, Liver, Kidney, Heart)
227
COVID-19 B cell and Plasma cell Atlas in PBMC and BAL
123
COVID-19 BAL Atlas
83
COVID-19 Cerebrospinal Fluid-derived (CSF) Leukecytes
179
COVID-19 Lung Atlas
222
COVID-19 Lung Autopsy Data (SCP1219)
116
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
Cells of the human intestinal tract mapped across space and time
1,269
Colon Immune Atlas
206
Colon Immune Atlas from Gut Cell Atlas
183
Comparison of human cortex and organoids
94
Cross-tissue immune cell analysis reveals tissue-specific features in humans
645
Human Adult Brain MTG
264
Human Blood Atlas
53
Human Bone Marrow Atlas
78
Human Bronchial Epithelial Cells (HBEC)
43
Human Cord Blood Atlas
81
Human Fetal Lung in Development
202
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)
1,193
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
946
Immune and Hematologic Cells from 24 tissues of the Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans.
416
Influenza Atlas
84
Integrated Single-nucleus and Single-cell RNA-seq of the Adult Human Kidney
1,467
Integration of 5 COVID-19 PBMC Datasets
124
Integration of Four Brain Organoid Datasets and One Fetal Brain Dataset
480
Integration of Lung Superbins
154
Integration of Multiple Sampling Location of COVID-19 Patients
1,421
Integration of immune-mediated diseases (COVID-19 + Influenza + Sepsis + Multiple Sclerosis)
384
Large Scale COVID-19 Single Cell Data (Ren et al.)
875
LungMAP — Genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the mouse lung
296
Mouse Adult Brain Overview (690k cells, 9 regions, 565 cell clusters)
1,672
Mouse Adult Trachea
46
Mouse Aging Atlas- Tabula Muris Senis
4,907
Mouse Aging Atlas- Tabula Muris Senis (Lung and Trachea)
888
Mouse Bone Marrow Niche (Baccin et al)
68
Mouse Bone Marrow Niche (Baryawno et al)
38
Mouse Bone Marrow Niche (Tikhonova et al)
29
Mouse Trachea Epithelial Cells (MTECs)
49
Mouse developmental Lung
102
Mouse_Lung_DevAtlas
153
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
PretermPrimateLungAtlas
295
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
Shared and distinct transcriptomic cell types across neocortical areas
293
TCGA OncoMap
773
The Integrated Human Lung Cell Atlas
2,345
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
381
mouse_P3_lung_dropseq (2716 cells)
69
scRNA-seq of ileum and lung epithelial cells in macaque.
9
Genes:
45,650
Coexpression
Annotations:
12,951
GeneSigDB
3,515
MSigDB C2: CGP Curated Gene Sets (v7.5.1)
3,384
MSigDB C6: Oncogenic Signatures (v7.5.1)
83
MSigDB C7: Immunologic Signatures (v7.5.1)
5,219
MSigDB C8: Cell Type Signatures (v7.5.1)
700
MSigDB H: Hallmark Gene Sets (v7.5.1)
50
Genes:
26,258
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:
21,235
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:
77,146
Broad Institute CMAP Down
6,100
Broad Institute CMAP Up
6,100
CTD
12,437
Drug Bank
3,803
Stitch
48,706
Genes:
22,767
Disease
Annotations:
42,637
Clinical Variations
6,909
DisGeNET BeFree
17,993
DisGeNET Curated
11,181
GWAS
291
OMIM MedGen
6,263
Genes:
19,383
Master Gene Info File
Updated Aug 2, 2022
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-p4