TCPA V3.0: An Integrative Platform to Explore the Pan-Cancer Analysis of Functional Proteomic Data

Overview

Journal Mol Cell Proteomics

Specialties Biochemistry
Cell Biology
Molecular Biology

Date 2019 Jun 16

PMID 31201206

Citations 32

Authors

Mei-Ju May Chen

Jun Li

Yumeng Wang

Rehan Akbani

Yiling Lu

Gordon B Mills

Han Liang

Affiliations

Soon will be listed here.

Abstract

Reverse-phase protein arrays represent a powerful functional proteomics approach to characterizing cell signaling pathways and understanding their effects on cancer development. Using this platform, we have characterized ∼8,000 patient samples of 32 cancer types through The Cancer Genome Atlas and built a widely used, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA). To maximize the utility of TCPA, we have developed a new module called "TCGA Pan-Cancer Analysis," which provides comprehensive protein-centric analyses that integrate protein expression data and other TCGA data across cancer types. We further demonstrate the value of this module by examining the correlations of RPPA proteins with significantly mutated genes, assessing the predictive power of somatic copy-number alterations, DNA methylation, and mRNA on protein expression, inferring the regulatory effects of miRNAs on protein expression, constructing a co-expression network of proteins and pathways, and identifying clinically relevant protein markers. This upgraded TCPA (v3.0) will provide the cancer research community with a more powerful tool for studying functional proteomics and making translational impacts.

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