Protocol for analysis of RNA-sequencing and proteome profiling data for subgroup identification and comparison

STAR Protoc. 2022 May 23;3(2):101283. doi: 10.1016/j.xpro.2022.101283. eCollection 2022 Jun 17.

Abstract

RNA-sequencing and quantitative proteomic profiling simultaneously measure thousands of molecules and provide opportunities to decipher the transcriptomic and proteomic landscapes of cohort specimens for basic and health research. We present a protocol for the analysis of paired transcriptome and proteome data to identify and compare molecular subgroups among cohort specimens. We demonstrate a streamlined analysis workflow, applicable for both transcriptome and proteome data, which allows the comparison of two data types for RNA-protein variations and for derivation of biological implications. For complete details on the use and execution of this protocol, please refer to Yang et al. (2021).

Keywords: Bioinformatics; Cancer; Gene Expression; Proteomics; RNAseq.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Humans
  • Proteome* / genetics
  • Proteomics* / methods
  • RNA / genetics
  • Sequence Analysis, RNA

Substances

  • Proteome
  • RNA

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