SLEPR: a sample-level enrichment-based pathway ranking method -- seeking biological themes through pathway-level consistency.

ABSTRACT: Analysis of microarray and other high throughput data often involves identification of genes consistently up or down-regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of

SUBMITTER: Yi M 

PROVIDER: S-EPMC2546449 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature