Loss of connectivity in cancer co-expression networks.
Differential gene expression profiling studies have lead to the identification of several disease biomarkers. However, the oncogenic alterations in coding regions can modify the gene functions without affecting their own expression profiles. Moreover, post-translational modifications can modify the activity of the coded protein without altering the expression levels of the coding gene, but eliciting variations to the expression levels of the regulated genes. These considerations motivate the study of the rewiring of networks co-expressed genes as a consequence of the aforementioned alterations in order to complement the informative content of differential expression. We analyzed 339 mRNAomes of five distinct cancer types to find single genes that presented co-expression patterns strongly differentiated between normal and tumor phenotypes. Our analysis of differentially connected genes indicates the loss of connectivity as a common topological trait of cancer networks, and unveils novel candidate cancer genes. Moreover, our integrated approach that combines the differential expression together with the differential connectivity improves the classic enrichment pathway analysis providing novel insights on putative cancer gene biosystems not still fully investigated.
Institute of Intelligent Systems for Automation, National Research Council, CNR-ISSIA, Bari, Italy.
Roberto
R
Anglani
Institute of Intelligent Systems for Automation, National Research Council, CNR-ISSIA, Bari, Italy ; Center for Complex Systems in Molecular Biology and Medicine, University of Torino, Torino, Italy.
Teresa M
TM
Creanza
Institute of Intelligent Systems for Automation, National Research Council, CNR-ISSIA, Bari, Italy.
Vania C
VC
Liuzzi
Department of Medical Sciences, Division and Laboratory of Gastroenterology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
Ada
A
Piepoli
Department of Medical Sciences, Division and Laboratory of Gastroenterology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
Anna
A
Panza
Department of Medical Sciences, Division and Laboratory of Gastroenterology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
Angelo
A
Andriulli
Institute of Intelligent Systems for Automation, National Research Council, CNR-ISSIA, Bari, Italy.
Nicola
N
Ancona
D014408:Biomarkers, Tumor / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D052138:Genes, Neoplasm; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics
D014408:Biomarkers, Tumor