Individualized pathway activity algorithm identifies oncogenic pathways in pan-cancer analysis.

ABSTRACT:

Background

Accumulative evidences have shown that dysregulation of biological pathways contributed to the initiation and progression of malignant tumours. Several methods for pathway activity measurement have been proposed, but they are restricted to making comparisons between groups or sensitive to experimental batch effects.

Methods

We introduced a novel method for individualized pathway activity measurement (IPAM) that is based on the ranking of gene expression levels in individual sample. Taking advantage of IPAM, we calculated the pathway activity of 318 pathways from KEGG database in the 10528 tumour/normal samples of 33 cancer types from TCGA to identify characteristic dysregulated pathways among different cancer types.

Findings

IPAM precisely quantified the le

SUBMITTER: Ke X 

PROVIDER: S-EPMC9117264 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature