CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

Wang, Qixuan; Huang, Jinyan; Sun, Hanfei; Liu, Jing; Wang, Juan; Wang, Qian; Qin, Qian; Mei, Shenglin; Zhao, Cong; Yang, Xiaoqin; Liu, X. Shirley; Zhang, Yong

doi:10.1093/nar/gkt1151

Cited by 43 publications

(52 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…tongji.edu.cn/cr and http://cistrome.org/cr/. 43 CR Cistrome is a ChIP-seq database for the CRs and histone modification (HM) linkages in human and mouse. This database is a collection of all publicly available ChIP-seq data on CRs in human and mouse.…”

Section: Perspectivementioning

confidence: 99%

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

et al. 2014

View full text Add to dashboard Cite

Section: Perspectivementioning

confidence: 99%

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

et al. 2014

View full text Add to dashboard Cite

“…These projects, however, do not support data generated outside the consortia. Other ChIP-seq databases, such as Cistrome CR (13), BloodChIP (14), CTCFBSDS (15), only contain a limited number of samples, each focusing on a narrow selection of factor or tissue types. Standardized quality control and streamlined analysis of ChIP-seq and chromatin accessibility data have also been lacking.…”

Section: Introductionmentioning

confidence: 99%

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

et al. 2016

Self Cite

View full text Add to dashboard Cite

Chromatin immunoprecipitation, DNase I hypersensitivity and transposase-accessibility assays combined with high-throughput sequencing enable the genome-wide study of chromatin dynamics, transcription factor binding and gene regulation. Although rapidly accumulating publicly available ChIP-seq, DNase-seq and ATAC-seq data are a valuable resource for the systematic investigation of gene regulation processes, a lack of standardized curation, quality control and analysis procedures have hindered extensive reuse of these data. To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromatin accessibility data (DNase-seq and ATAC-seq) published before January 1, 2016, including 13 366 human and 9953 mouse samples. All the data have been carefully curated and processed with a streamlined analysis pipeline and evaluated with comprehensive quality control metrics. We have also created a user-friendly web server for data query, exploration and visualization. The resulting Cistrome DB (Cistrome Data Browser), available online at http://cistrome.org/db, is expected to become a valuable resource for transcriptional and epigenetic regulation studies.

show abstract

“…To select genes encoding transcription factors we used TFClass database [37]. To classify genes as a transcriptional regulators we used the list of 167 genes encoding proteins with chromatin-modifying activities that was compiled previously [38] from three databases: EntrezGene (http://www.ncbi.nlm.nih.gov/gene), CREMOFAC [39], and CR Cistrome [40]. To annotate genes encoding proteins related to the cilium or BBSome, we used genes extracted from EntrezGene utilizing the GO terms “BBSome” or “cilium” as a query.…”

Section: Methodsmentioning

confidence: 99%

A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network

et al. 2016

View full text Add to dashboard Cite

BackgroundObesity is heritable. It predisposes to many diseases. The objectives of this study were to create a compendium of genes relevant to feeding behavior (FB) and/or body weight (BW) regulation; to construct and to analyze networks formed by associations between genes/proteins; and to identify the most significant genes, biological processes/pathways, and tissues/organs involved in BW regulation.ResultsThe compendium of genes controlling FB or BW includes 578 human genes. Candidate genes were identified from various sources, including previously published original research and review articles, GWAS meta-analyses, and OMIM (Online Mendelian Inheritance in Man). All genes were ranked according to knowledge about their biological role in body weight regulation and classified according to expression patterns or functional characteristics. Substantial and overrepresented numbers of genes from the compendium encoded cell surface receptors, signaling molecules (hormones, neuropeptides, cytokines), transcription factors, signal transduction proteins, cilium and BBSome components, and lipid binding proteins or were present in the brain-specific list of tissue-enriched genes identified with TSEA tool. We identified 27 pathways from KEGG, REACTOME and BIOCARTA whose genes were overrepresented in the compendium. Networks formed by physical interactions or homological relationships between proteins or interactions between proteins involved in biochemical/signaling pathways were reconstructed and analyzed. Subnetworks and clusters identified by the MCODE tool included genes/proteins associated with cilium morphogenesis, signal transduction proteins (particularly, G protein–coupled receptors, kinases or proteins involved in response to insulin stimulus) and transcription regulation (particularly nuclear receptors). We ranked GWAS genes according to the number of neighbors in three networks and revealed 22 GWAS genes involved in the brain-specific PPI network. On the base of the most reliable PPIs functioning in the brain tissue, new regulatory schemes interpreting relevance to BW regulation are proposed for three GWAS genes (ETV5, LRP1B, and NDUFS3). ConclusionsA compendium comprising 578 human genes controlling FB or BW was designed, and the most significant functional groups of genes, biological processes/pathways, and tissues/organs involved in BW regulation were revealed. We ranked genes from the GWAS meta-analysis set according to the number and quality of associations in the networks and then according to their involvement in the brain-specific PPI network and proposed new regulatory schemes involving three GWAS genes (ETV5, LRP1B, and NDUFS3) in BW regulation. The compendium is expected to be useful for pathology risk estimation and for design of new pharmacological approaches in the treatment of human obesity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0466-2) contains supplementary material, which is available to authorized users.

show abstract

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

Cited by 43 publications

References 55 publications

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network

Contact Info

Product

Resources

About