Explore, Visualize, and Analyze Functional Cancer Proteomic Data Using the Cancer Proteome Atlas

Abstract

Reverse-phase protein arrays (RPPA) represent a powerful functional proteomic approach to elucidate cancer-related molecular mechanisms and to develop novel cancer therapies. To facilitate community-based investigation of the large-scale protein expression data generated by this platform, we have developed a user-friendly, open-access bioinformatic resource, The Cancer Proteome Atlas (TCPA, http://tcpaportal.org), which contains two separate web applications. The first one focuses on RPPA data of patient tumors, which contains >8,000 samples of 32 cancer types from The Cancer Genome Atlas and other independent patient cohorts. The second application focuses on the RPPA data of cancer cell lines and contains >650 independent cell lines across 19 lineages. Many of these cell lines have publicly available, high-quality DNA, RNA, and drug screening data. TCPA provides various analytic and visualization modules to help cancer researchers explore these datasets and generate testable hypotheses in an effective and intuitive manner. Cancer Res; 77(21); e51-54. ©2017 AACR.

Figure 1

Overview of The Cancer Proteome Atlas (A) Information flow of RPPA data; (B) Overview of TCPA portal; (C) “Summary” module; (D) “Download” module; (E) “My Protein” module for patient-cohort data; (F) “My Protein” module for cell-line data; (G) “Correlation Analysis” for patient-cohort data; (H) “Correlation Analysis” module for cell-line data; (I) “Differential Expression” module for patient-cohort data; (J) “Patient Survival” module; (K) “Drug-Protein” module by protein; (L) “Drug-Protein” module by drug; (M) Zoomed-in view of “Network” visualization for patient-cohort data with a snapshot of the full view at the top-left corner; (N) Zoomed-in view of “Network” visualization for cell-line data; and (O) “NG-CHM” visualization with a snapshot of the full view at the top-left corner.