A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.

ABSTRACT: Protein expression and post-translational modification levels are tightly regulated in neoplastic cells to maintain cellular processes known as 'cancer hallmarks'. The first Pan-Cancer initiative of The Cancer Genome Atlas (TCGA) Research Network has aggregated protein expression profiles for 3,467 patient samples from 11 tumor types using the antibody based reverse phase protein array (RPPA) technology. The resultant proteomic data can be utilized to computationally infer protein-protein interaction (PPI) networks and to study the commonalities and differences across tumor types. In this study, we compare the performance of 13 established network inference methods in their capacity to retrieve the curated Pathway Commons interactions from RPPA data. We observe that no single method has th

SUBMITTER: Senbabaoglu Y 

PROVIDER: S-EPMC4771175 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature