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Prostate cancer gene regulatory network inferred from RNA-seq data

Research output: Contribution to journalArticleScientificpeer-review

Details

Original languageEnglish
Pages (from-to)38-48
Number of pages11
JournalCURRENT GENOMICS
Volume20
Issue number1
DOIs
Publication statusPublished - 2019
Publication typeA1 Journal article-refereed

Abstract

Background: Cancer is a complex disease with a lucid etiology and in understanding the causation, we need to appreciate this complexity. Objective: Here we are aiming to gain insights into the genetic associations of prostate cancer through a network-based systems approach using the BC3Net algorithm. Methods: Specifically, we infer a prostate cancer Gene Regulatory Network (GRN) from a large-scale gene expression data set of 333 patient RNA-seq profiles obtained from The Cancer Genome Atlas (TCGA) database. Results: We analyze the functional components of the inferred network by extracting subnetworks based on biological process information and interpret the role of known cancer genes within each process. Furthermore, we investigate the local landscape of prostate cancer genes and discuss pathological associations that may be relevant in the development of new targeted cancer therapies. Conclusion: Our network-based analysis provides a practical systems biology approach to reveal the collective gene-interactions of prostate cancer. This allows a close interpretation of biological activity in terms of the hallmarks of cancer.

ASJC Scopus subject areas

Keywords

  • Data science, Gene regulatory network, Genomics, Network inference, Precision medicine, Prostate cancer, Systems biology

Publication forum classification

Field of science, Statistics Finland