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:
16,580
Genes:
20,649
Updated Nov 30, 2023
GO Cellular Component
Annotations:
2,051
Genes:
20,915
Updated Nov 30, 2023
GO Molecular Function
Annotations:
5,247
Genes:
19,912
Updated Nov 30, 2023
Human Phenotype
Annotations:
11,291
Genes:
5,010
Updated Nov 30, 2023
Mouse Phenotype
Annotations:
11,283
Genes:
13,498
Updated Nov 29, 2023
Pathways
Annotations:
5,496
BioCarta Pathways
544
Canonical Pathways
19
KEGG Legacy Pathways
186
KEGG Medicus Pathways
619
PID Pathways
196
Reactome Pathways
2,953
WikiPathways
979
Genes:
13,850
Domains
Annotations:
21,882
Gene3D
861
InterPro
12,478
PROSITE
1,698
Pfam
5,691
ProDom
177
SMART
977
Genes:
18,677
Pubmed
Annotations:
1,088,807
Genes:
34,789
Updated Sep 11, 2023
Interactions
Annotations:
20,010
Genes:
20,010
Updated Nov 30, 2023
Cytoband
Annotations:
2,570
Genes:
45,858
TFBS
Annotations:
1,133
MSigDB
518
TFBS
615
Genes:
26,909
miRNA
Annotations:
10,743
MSigDB
313
MicroRNA.org
2,200
MirDB
4,632
PITA
677
TargetScan
322
miRTarbase
2,599
Genes:
57,446
Gene Families
Annotations:
940
Genes:
18,080
ToppCell Atlas
Annotations:
32,176
A Cellular Census of Human Lungs (Vieira Braga et al)
249
A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche
847
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
429
Airway Inflammation in Cystic Fibrosis (CF)
42
Atlas of Lymphangioleiomyomatosis (LAM)
40
Blood and immune development in human fetal bone marrow
511
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
1,671
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
610
Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma
668
Human Adult Brain MTG
264
Human Adult Multiple Cortical Areas SMART-seq
867
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)
615
Human Lung Cells in 3 Age Groups (Wang et al.)
414
Human Metastatic Lung Adenocarcinoma (Nayoung Kim et al)
526
Human embryonic and fetal stage lung cell atlas
398
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 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_Lung_DevAtlas
153
Mouse_Lung_DropSeq_E16-P28
982
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
Single-cell RNA-seq reveals the cell-type-specific molecular and genetic associations to lupus
301
TCGA OncoMap
773
The Integrated Human Lung Cell Atlas
1,216
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:
44,952
Coexpression
Annotations:
10,922
C2:CGP: Chemical and Genetic Perturbations
3,438
C6: Oncogenic Signature
189
C7:IMMUNESIGDB: ImmuneSigDB
4,872
C7:VAX: HIPC Vaccine Response
347
C8: Cell Type Signature
830
H: Hallmark
50
M2:CGP: Chemical and Genetic Perturbations
963
M8: Cell Type Signature
233
Genes:
26,205
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:
21,234
Computational Gene Set
Annotations:
1,007
C4:3CA: Curated Cancer Cell Atlas gene sets
149
C4:CGN: Cancer Gene Neighborhoods
427
C4:CM: Cancer Modules
431
Genes:
10,746
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:
22,768
Disease
Annotations:
44,167
AllianceGenome
9,343
Clinical Variations
7,256
DisGeNET Curated
11,181
GWAS
9,808
OMIM MedGen
6,579
Genes:
29,485
Master Gene Info File
Updated Nov 30, 2023
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