comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines综合分析基因组的转录组和蛋白质组三个肿瘤细胞系的风景.pdfVIP

Akan et al. Genome Medicine 2012, 4:86 /content/4/11/86 METHOD Open Access 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 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. Background cells of mesenchymal origin that differentiate to osteo- Human cancer cell lines have been an invaluable and blasts. It is the most common form of bone cancer, practical resource for cancer research. The availability of responsible for 2.4% of all malignancies in pediatric genomic, transcriptomic and proteomic data on these patients, and its triggers are currently not known [5]. lines is expected to further increase their utility. To this U2OS is a common choice for osteosarcoma research: end, we conducted whole-genome and transcriptome 35% of the articles associated wit