Welcome to scGRN!
A comprehensive single-cell gene regulatory network platform of human and mouse
What is scGRN?
Here, we present scGRN (https://bio.liclab.net/scGRN/), a comprehensive single-cell multi-omics gene regulatory network platform of human and mouse.
The current version of scGRN catalogs a total of 62,999,692 cell type-specific TF-target gene pairs, covering 163 tissues/cell lines and 6,808,724 cells from 1,324 single-cell multi-omics samples. These samples (scRNA-seq and scATAC-seq) have been manually curated from NCBI GEO/SRA, ENCODE and Arrayexpress databases, including multiple single-cell sequencing platforms. We have performed quality control for each sample to ensure the quality of the data in scGRN. A unified pipeline and software parameters were used for GRN inference form scRNA-seq and scATAC-seq data, respectively. scGRN provides visualizations such as clustering, cell type annotation, heatmap of transcription factor activity, and inferred cell type-specific GRNs for each sample. Moreover, scGRN also provides details about TFs binding to promoters, super-enhancers and typical enhancers of target gene in GRNs. Taken together, scGRN is an integrative and useful platform for searching, browsing, analyzing, visualizing, and downloading GRNs of interest. We anticipate that scGRN will become an integrative and useful platform for exploring potential functions and regulatory mechanisms in disease and biological processes.
Tissue distribution
Statistics
Principal Investigator: Chunquan Li, Ph.D.
The First Affiliated Hospital, Hengyang Medical School, University of South China
Email: lcqbio@163.com
We welcome researchers from all over the world to provide valuable advice for scGRN and make scGRN more and more perfect.
KnockTF
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors
LncSEA
LncSEA: A comprehensive human lncRNA sets resource and enrichment analysis platform
SEdb
SEdb: The comprehensive human Super-Enhancer databasebr
SEanalysis
SEanalysis: a web tool for super-enhancer associated regulatory analysis
ENdb
ENdb: An experimentally supported enhancer database for human and mouse
VARAdb
VARAdb: A comprehensive human variation annotation database
TRlnc
TRlnc: A comprehensive database of human transcriptional regulation of lncRNAs
TRCirc
TRCirc: A resource for transcriptional regulation information of circRNAs
ATACdb
ATACdb: A comprehensive human chromatin accessibility database
TcoFbase
TcoFbase: Document a large number of available resources of mammals TcoFs