Utility and Limitations of Using Gene Expression Data to Identify Functional Associations.

ABSTRACT: Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the abil

SUBMITTER: Uygun S 

PROVIDER: S-EPMC5147789 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature