Testing the Significance of Ranked Gene Sets in Genome-wide Transcriptome Profiling Data Using Weighted Rank Correlation Statistics.

ABSTRACT:

Background

Popular gene set enrichment analysis approaches assumed that genes in the gene set contributed to the statistics equally. However, the genes in the transcription factors (TFs) derived gene sets, or gene sets constructed by TF targets identified by the ChIP-Seq experiment, have a rank attribute, as each of these genes have been assigned with a p-value which indicates the true or false possibilities of the ownerships of the genes belong to the gene sets.

Objectives

Ignoring the rank information during the enrichment analysis will lead to improper statistical inference. We address this issue by developing of new method to test the significance of ranked gene sets in genome-wide transcriptome profiling data.

Methods

A method was proposed by first creating ranke

SUBMITTER: Yao M 

PROVIDER: S-EPMC11288161 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature