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Article: CR2Cancer: a database for chromatin regulators in human cancer
Title | CR2Cancer: a database for chromatin regulators in human cancer |
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Authors | |
Issue Date | 2018 |
Publisher | Oxford University Press (OUP): Policy C - Option B. The Journal's web site is located at http://nar.oxfordjournals.org/ |
Citation | Nucleic Acids Research, 2018, v. 46 n. D1, p. D918-D924 How to Cite? |
Abstract | Identification of Master Regulators (MRs) during cancer development contributes greatly to the design of novel targeted therapy. However, it is challenging to trace the MR that regulate the gene signature (e.g. differentially expressed genes) derived from a limited number of transcriptome profiles. The main reason is that the targets (collectively termed as regulon) of MRs in cancer type-specific context is not available for enrichment analysis in the signature. To this aim, we generated the regulon of MRs using high throughput omics data from The Cancer Genome Atlas (TCGA), and developed a web server MR4Cancer, which can prioritize MRs driving phenotypic differentiation of interest in 26 cancer types. Based on the input gene list or expression profiles, it outputs six groups of ranked MRs, including transcription regulators, miRNAs, recurrently mutated genes, kinases, phosphatases, and hubs from protein-protein interaction network. Simultaneously, Gene Ontology and canonical pathway analyses are also conducted to further elucidate the function of MR candidates. Moreover, our tool presents dynamic network visualization for MR-target relations, and users can interactively customize it as high quality figures for their publications. We expect this user-friendly and powerful web application will provide researchers new insights into carcinogenesis and therapeutic intervention. |
Persistent Identifier | http://hdl.handle.net/10722/249561 |
ISSN | 2023 Impact Factor: 16.6 2023 SCImago Journal Rankings: 7.048 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | RU, B | - |
dc.contributor.author | SUN, J | - |
dc.contributor.author | TONG, Y | - |
dc.contributor.author | Wong, CN | - |
dc.contributor.author | Chandra, A | - |
dc.contributor.author | Tang, ATS | - |
dc.contributor.author | Chow, LKY | - |
dc.contributor.author | Wun, WL | - |
dc.contributor.author | Levitskaya, Z | - |
dc.contributor.author | Zhang, J | - |
dc.date.accessioned | 2017-11-21T03:03:55Z | - |
dc.date.available | 2017-11-21T03:03:55Z | - |
dc.date.issued | 2018 | - |
dc.identifier.citation | Nucleic Acids Research, 2018, v. 46 n. D1, p. D918-D924 | - |
dc.identifier.issn | 0305-1048 | - |
dc.identifier.uri | http://hdl.handle.net/10722/249561 | - |
dc.description.abstract | Identification of Master Regulators (MRs) during cancer development contributes greatly to the design of novel targeted therapy. However, it is challenging to trace the MR that regulate the gene signature (e.g. differentially expressed genes) derived from a limited number of transcriptome profiles. The main reason is that the targets (collectively termed as regulon) of MRs in cancer type-specific context is not available for enrichment analysis in the signature. To this aim, we generated the regulon of MRs using high throughput omics data from The Cancer Genome Atlas (TCGA), and developed a web server MR4Cancer, which can prioritize MRs driving phenotypic differentiation of interest in 26 cancer types. Based on the input gene list or expression profiles, it outputs six groups of ranked MRs, including transcription regulators, miRNAs, recurrently mutated genes, kinases, phosphatases, and hubs from protein-protein interaction network. Simultaneously, Gene Ontology and canonical pathway analyses are also conducted to further elucidate the function of MR candidates. Moreover, our tool presents dynamic network visualization for MR-target relations, and users can interactively customize it as high quality figures for their publications. We expect this user-friendly and powerful web application will provide researchers new insights into carcinogenesis and therapeutic intervention. | - |
dc.language | eng | - |
dc.publisher | Oxford University Press (OUP): Policy C - Option B. The Journal's web site is located at http://nar.oxfordjournals.org/ | - |
dc.relation.ispartof | Nucleic Acids Research | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.title | CR2Cancer: a database for chromatin regulators in human cancer | - |
dc.type | Article | - |
dc.identifier.email | Zhang, J: jzhang1@hku.hk | - |
dc.identifier.authority | Zhang, J=rp01713 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1093/nar/gkx877 | - |
dc.identifier.scopus | eid_2-s2.0-85040946023 | - |
dc.identifier.hkuros | 282997 | - |
dc.identifier.volume | 46 | - |
dc.identifier.issue | D1 | - |
dc.identifier.spage | D918 | - |
dc.identifier.epage | D924 | - |
dc.identifier.isi | WOS:000419550700134 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 0305-1048 | - |