A comprehensive human chromatin regulator database
Here, we developed the CRdb database (http://cr.liclab.net/crdb), which aimed to record a large number of available resources for CRs, and provided extensive annotations and analysis of CRs.
The current version of CRdb collected a total of 647 CRs and 2,591 CRs associated ChIP-seq data from more than 300 human tissues and cell types. These samples have been manually curated from NCBI GEO/SRA and ENCODE. CRdb emphatically provided the circumstantial and numerous (epi) genetic annotations in CR-binding regions by processing and integrating large-scale high/low-throughput experimental data, including super-enhancers, enhancers, transcription factor binding sites (TFBS), methylation sites, common single nucleotide polymorphisms (SNPs), risk SNPs, expression quantitative trait locus (eQTL), 3D chromatin interactions and accessible chromatin. CRdb also provided CR downstream target genes via five methods. Furthermore, CRdb supported upstream regulatory information and various functional annotations of CRs, including Gene Ontology (GO) terms, pathways, protein-protein interactions (PPIs), cancer hallmarks, survival, disease information and gene expression. In particular, CRdb embedded four types of CR regulatory analyses for users, including CR gene set enrichment, CR binding genomic region annotation, CR-TF co-occupancy analysis and CR regulatory axis analysis. CRdb can become a serviceable and powerful platform to explore the underlying functions and regulatory mechanisms of CRs in diseases and biological processes.
ENdb
ENdb: an experimentally supported enhancer database for human and mouse
SEanalysis
SEanalysis: a web tool for super-enhancer associated regulatory analysis
VARAdb
VARAdb: a variation annotation database for human
ATACdb
ATACdb: a comprehensive human chromatin accessibility database
SEdb
SEdb: the comprehensive human Super-Enhancer database
TcoFbase
TcoFbase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse.
KnockTF
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription
factors
TRCirc
TRCirc: a resource for transcriptional regulation information of circRNAs
TRlnc
TRlnc: a comprehensive database of human transcriptional regulation of lncRNAs
LncSEA
LncSEA: a comprehensive human lncRNA sets resource and enrichment analysis platform
TF-Maker
TF-Maker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human
CR | The Number of Sources | 2 |
The Number of CRs | 647 | |
CR(ChIP-seq) | The Number of Sources | 2 |
The Number of CRs | 183 | |
The Number of Samples | 2591 | |
TF(Motif) | The Number of Sources | 6 |
The Number of TFs | 699 | |
The Number of Motifs | 3279 | |
Pathway | The Number of Sources | 10 |
The Number of Pathways | 2169 |
Principal Investigator: Chunquan Li, Ph.D.
Email: lcqbio@163.com
The First Affiliated Hospital, Hengyang Medical School, University of South China School of Computer, University of South China