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Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines

Pelin Akan*, Andrey Alexeyenko, Paul Igor Costea, Lilia Hedberg, Beata Werne Solnestam, Sverker Lundin, Jimmie Hällman, Emma Lundberg, Mathias Uhlén and Joakim Lundeberg

Author Affiliations

KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden

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Genome Medicine 2012, 4:86  doi:10.1186/gm387

Published: 18 November 2012


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.