GeneTopics--interpretation of gene sets via literature-driven topic models.

ABSTRACT:

Background

Annotation of a set of genes is often accomplished through comparison to a library of labelled gene sets such as biological processes or canonical pathways. However, this approach might fail if the employed libraries are not up to date with the latest research, don't capture relevant biological themes or are curated at a different level of granularity than is required to appropriately analyze the input gene set. At the same time, the vast biomedical literature offers an unstructured repository of the latest research findings that can be tapped to provide thematic sub-groupings for any input gene set.

Methods

Our proposed method relies on a gene-specific text corpus and extracts commonalities between documents in an unsupervised manner using a topic model approach.

SUBMITTER: Wang V 

PROVIDER: S-EPMC4029197 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature