CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

Qin, Bo; Zhou, Meng; Ge, Ying; Taing, Len; Liu, Tao; Wang, Qian; Wang, Su; Chen, Junsheng; Shen, Litao; Duan, Xikun; Hu, Shengen; Li, Wei; Long, Henry W.; Zhang, Yong; Liu, X. Shirley

doi:10.1093/bioinformatics/bts157

Cited by 36 publications

(34 citation statements)

References 8 publications

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“…CistromeMap database (http://cistrome.org/pc/) was used for the query of publicly available ChIP-seq datasets (13). E2F1 and BRCA1 ChIP-seq datasets from ENCODE cell lines were downloaded from UCSC genome browser databases.…”

Section: Methodsmentioning

confidence: 99%

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

Zang

et al. 2016

Molecular Cancer Research

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Overexpression of EZH2 is frequently linked to the advanced and metastatic stage of cancers. The mechanisms of its oncogenic function can be context specific, and may vary depending on the protein complexes that EZH2 interacts with. To identify novel transcriptional collaborators of EZH2 in cancers, a computational approach was developed that integrates protein-DNA binding data, cell perturbation gene expression data, and compendiums of tumor expression profiles. This holistic approach identified E2F1, a known mediator of the Rb tumor suppressor, as a transcriptional collaborator of EZH2 in castration-resistant prostate cancer. Subsequent analysis and experimental validation found EZH2 and E2F1 cobind to a subset of chromatin sites lacking H3K27 trimethylation, and activate genes that are critical for prostate cancer progression. The collaboration of EZH2 and E2F1 in transcriptional regulation is also observed in diffuse large B-cell lymphoma cell lines, where activation of the transcriptional network is concordant with the cellular response to the EZH2 inhibitor. Implications:The direct collaboration between EZH2 and Rb/E2F1 pathway provides an innovative mechanism underlying the cascade of tumor progression, and lays the foundation for the development of new anticancer targets/strategies.

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Section: Methodsmentioning

confidence: 99%

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

Zang

et al. 2016

Molecular Cancer Research

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“…We manually collected and integrated 3785 high throughput experimental datasets (Table 1) mainly from six resources including UCSC genome browser (Kent et al, 2002), NCBI GEO (Barrett et al, 2013), Cistrome database (Qin et al, 2012), ENCODE project data portal (Consortium, 2012), Epigenome Roadmap data portal (Roadmap Epigenomics et al, 2015) and eRNA (Andersson et al, 2014). These datasets will be used to generate consensus enhancers for 105 cell/tissue types.…”

Section: Selection Of Available Datasetsmentioning

confidence: 99%

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types

et al. 2016

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Motivation: Multiple high-throughput approaches have recently been developed and allowed the discovery of enhancers on a genome scale in a single experiment. However, the datasets generated from these approaches are not fully utilized by the research community due to technical challenges such as lack of consensus enhancer annotation and integrative analytic tools. Results: We developed an interactive database, EnhancerAtlas, which contains an atlas of 2,534,123 enhancers for 105 cell/tissue types. A consensus enhancer annotation was obtained for each cell by summation of independent experimental datasets with the relative weights derived from a cross-validation approach. Moreover, EnhancerAtlas provides a set of useful analytic tools that allow users to query and compare enhancers in a particular genomic region or associated with a gene of interest, and assign enhancers and their target genes from a custom dataset. Availability and Implementation: The database with analytic tools is available at http://www.enhan ceratlas.org/.

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“…Once the puri fi ed and enriched DNA fragments are obtained, high-throughput sequencing is performed and fragments of 50-100mers are mapped back to the reference genome. Currently, deep sequencing technology can sequence up to 100 million reads for a given experiment, and this number is very likely to increase exponentially while the overall cost of sequencing will drop over the next 5-10 years [ 17,18 ] . Analyzing deep sequencing data for a particular ChIP experiment requires several important steps, which include initial quality control, peak calling, peak quality assessment, motif analysis, and large prediction and annotations of the data [ 17 ] .…”

Section: Advancement In Sequencing Technology Allows For Comprehensivmentioning

confidence: 99%

“…Interestingly, the tagSNPs are distributed among many chromosomes (Fig. 5.4a ) with the exception being that chromosomes 1,14,15,16,18,20, and 21 do not contain any tagSNPs. They occur at relatively gene rich areas (inner circle of Fig.…”

Section: Gwas Pcamentioning

confidence: 99%

The Functionality of Prostate Cancer Predisposition Risk Regions Is Revealed by AR Enhancers

Noushmehr

Coetzee

Rhie

et al. 2013

Androgen-Responsive Genes in Prostate Cancer

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Prostate Cancer (PCa) genetic risk has recently been de fi ned in numerous genome-wide association studies (GWAS), which revealed more than 50 diseaseassociated single nucleotide polymorphisms (SNPs), known as tagSNPs, each at a different locus. More than 80% of these tagSNPs are located in noncoding regions of the genome for which functionality remains unknown. We and others hypothesize that at least some of these SNPs affect noncoding genomic regulatory signatures such as enhancers. Many research laboratories including ours have pro fi led the genomic

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CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

Cited by 36 publications

References 8 publications

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types

The Functionality of Prostate Cancer Predisposition Risk Regions Is Revealed by AR Enhancers

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