TY - JOUR T1 - An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer A1 - Nibbe, Rod K. A1 - Koyutürk, Mehmet A1 - Chance, Mark R. Y1 - 2010/01/15 N2 - Author Summary Intensive research on cancer has led to an understanding of many individual genes that may be important for the initiation and progression of tumors. However, since cancer is a progressive disease that results from accumulation of multiple mutations likely acting in concert, individual markers can only provide limited insights into cellular mechanisms that underlie tumorigenesis. For this reason, recent studies focus on identification of “sub-network markers”, that is, functionally associated genes that exhibit coordinate changes in molecular expression during cancer progression. However, expression of genes is most frequently interrogated at the mRNA level, which captures functional activity of genes only to a limited extent. Screening of protein expression, on the other hand, provides information on the abundance of functional gene products, but its scale is often limited compared to screening of mRNA expression. In this article, we develop a proteomics-driven computational method that searches for sub-network markers in human colorectal cancer, based on a seed of differentially expressed proteins identified by proteomic screening. Our results show that significant changes in the expression of these proteins is likely to be associated with coordinate changes in the expression of the genes whose products are functionally associated with these proteins. This analysis leads to novel insights in the synergistic processes that underlie tumorigenesis. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 6 IS - 1 UR - https://doi.org/10.1371/journal.pcbi.1000639 SP - e1000639 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000639 ER -