biostudies-literatureYang KCCIHR101283https://www.ebi.ac.uk/biostudies/studies/S-EPMC9133752biostudies-literatureUnknown3(2)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).STAR protocolsProtocol for analysis of RNA-sequencing and proteome profiling data for subgroup identification and comparison.PMC9133752PJT-159536Gorski SMYang KCfalseProtocol for analysis of RNA-sequencing and proteome profiling data for subgroup identification and comparison.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).2022-01-01T00:00:00Z2022 Jun2025-04-04T13:29:39.725Z2024-11-13T05:15:57.515ZS-EPMC91337523563436110.1016/j.xpro.2022.101283