Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer.
chromatin interaction
enhancer
epigenetics
histone modification
network analysis
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2021
2021
Historique:
received:
05
02
2021
accepted:
29
03
2021
entrez:
17
6
2021
pubmed:
18
6
2021
medline:
18
6
2021
Statut:
epublish
Résumé
Regulation of gene expression through multiple epigenetic components is a highly combinatorial process. Alterations in any of these layers, as is commonly found in cancer diseases, can lead to a cascade of downstream effects on tumor suppressor or oncogenes. Hence, deciphering the effects of epigenetic alterations on regulatory elements requires innovative computational approaches that can benefit from the huge amounts of epigenomic datasets that are available from multiple consortia, such as Roadmap or BluePrint. We developed a software tool named IRENE (Integrative Ranking of Epigenetic Network of Enhancers), which performs quantitative analyses on differential epigenetic modifications through an integrated, network-based approach. The method takes into account the additive effect of alterations on multiple regulatory elements of a gene. Applying this tool to well-characterized test cases, it successfully found many known cancer genes from publicly available cancer epigenome datasets.
Identifiants
pubmed: 34135941
doi: 10.3389/fgene.2021.664654
pmc: PMC8201988
doi:
Types de publication
Journal Article
Langues
eng
Pagination
664654Informations de copyright
Copyright © 2021 Wang, Wu, Vorberg, Eils and Herrmann.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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