title: Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.
abstract: We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Pelin
authors.initials: P
authors.lastname: Akan
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Andrey
authors.initials: A
authors.lastname: Alexeyenko
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Paul Igor
authors.initials: PI
authors.lastname: Costea
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Lilia
authors.initials: L
authors.lastname: Hedberg
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Beata Werne
authors.initials: BW
authors.lastname: Solnestam
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Sverker
authors.initials: S
authors.lastname: Lundin
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Jimmie
authors.initials: J
authors.lastname: Hällman
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Emma
authors.initials: E
authors.lastname: Lundberg
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlén
authors.affiliation: KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg