title: Decoding transcriptional states in cancer.
abstract: Gene regulatory networks determine cellular identity. In cancer, aberrations of gene networks are caused by driver mutations that often affect transcription factors and chromatin modifiers. Nevertheless, gene transcription in cancer follows the same cis-regulatory rules as normal cells, and cancer cells have served as convenient model systems to study transcriptional regulation. Tumours often show regulatory heterogeneity, with subpopulations of cells in different transcriptional states, which has important therapeutic implications. Here, we review recent experimental and computational techniques to reverse engineer cancer gene networks using transcriptome and epigenome data. New algorithms, data integration strategies, and increasing amounts of single cell genomics data provide exciting opportunities to model dynamic regulatory states at unprecedented resolution.
authors.affiliation: Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium.
authors.forename: Jasper
authors.initials: J
authors.lastname: Wouters
authors.affiliation: Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium.
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Kalender Atak
authors.affiliation: Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium. Electronic address: stein.aerts@kuleuven.vib.be.
authors.forename: Stein
authors.initials: S
authors.lastname: Aerts
mesh_terms: D001665:Binding Sites; D019295:Computational Biology; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks / Q000235:genetics*; D023281:Genomics; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors