Network perturbation by recurrent regulatory variants in cancer

Kiwon Jang, Kwoneel Kim, Ara Cho, Insuk Lee, Jung Kyoon Choi

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

Abstract

Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences. However, a majority of cancer variants arise in noncoding regions, and some of them are thought to play a critical role through transcriptional perturbation. Here we identified putative transcriptional driver genes based on combinatorial variant recurrence in cis-regulatory regions. The identified genes showed high connectivity in the cancer type-specific transcription regulatory network, with high outdegree and many downstream genes, highlighting their causative role during tumorigenesis. In the protein interactome, the identified transcriptional drivers were not as highly connected as coding driver genes but appeared to form a network module centered on the coding drivers. The coding and regulatory variants associated via these interactions between the coding and transcriptional drivers showed exclusive and complementary occurrence patterns across tumor samples. Transcriptional cancer drivers may act through an extensive perturbation of the regulatory network and by altering protein network modules through interactions with coding driver genes.

Original languageEnglish
Article numbere1005449
JournalPLoS computational biology
Volume13
Issue number3
DOIs
Publication statusPublished - 2017 Mar

Bibliographical note

Funding Information:
This work was supported by the ?Development of biomedical data network analysis technology based on high performance computing for dementia researches (K-16-L03-C02-S02)? funded by KISTI, and by a grant from the Korea Healthcare Technology R&D Project, Ministry for Health & Welfare Affairs (HI13C0715). Research facilities were supported by the CHUNG Moon Soul Center of KAIST and by the Data Computing Project of KISTI-GSDC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© 2017 Jang et al.

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Modelling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

Fingerprint Dive into the research topics of 'Network perturbation by recurrent regulatory variants in cancer'. Together they form a unique fingerprint.

Cite this