PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling

Background: Colon cancer is driven by mutations in a number of genes, the most notorious of which is Apc. Though much of Apc's signaling has been mechanistically identified over the years, it is not always clear which functions or interactions are operative in a particular tumor. This is confounded by the presence of mutations in a number of other putative cancer driver (CAN) genes, which often synergize with mutations in Apc. Computational methods are, thus, required to predict which pathways are likely to be operative when a particular mutation in Apc is observed. Results: We developed a pipeline, PETALS, to predict and test likely signaling pathways connecting Apc to other CAN-genes, where the interaction network originating at Apc is defined as a "blossom," with each Apc-CAN-gene subnetwork referred to as a "petal." Known and predicted protein interactions are used to identify an Apc blossom with 24 petals. Then, using a novel measure of bimodality, the co...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Gürkan Bebek, Vishal Patel, Mark R. Chance
• Keywords: BMCBI 2010, Business, Cancer, Mutations, Petal