Immune depletion of the methylated phenotype of colon cancer is closely related to resistance to immune checkpoint inhibitors.

ABSTRACT:

Background

Molecular typing based on single omics data has its limitations and requires effective integration of multiple omics data for tumor typing of colorectal cancer (CRC).

Methods

Transcriptome expression, DNA methylation, somatic mutation, clinicopathological information, and copy number variation were retrieved from TCGA, UCSC Xena, cBioPortal, FireBrowse, or GEO. After pre-processing and calculating the clustering prediction index (CPI) with gap statistics, integrative clustering analysis was conducted via MOVICS. The tumor microenvironment (TME) was deconvolved using several algorithms such as GSVA, MCPcounter, ESTIMATE, and PCA. The metabolism-relevant pathways were extracted through ssGSEA. Differential analysis was based on limma and enrichment analysis w

SUBMITTER: Zhong C 

PROVIDER: S-EPMC9492852 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature