TCPA v3.0: An integrative platform to explore the pan-cancer analysis of functional proteomic data

Mei Ju May Chen, Jun Li, Yumeng Wang, Rehan Akbani, Yiling Lu, Gordon B. Mills, Han Liang

Research output: Contribution to journalArticlepeer-review

41 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)S15-S25
JournalMolecular and Cellular Proteomics
Issue number8
StatePublished - 2019

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology


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