CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments.

ABSTRACT:

Background

Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or using the GO structure to classify experiments has received little attention.

Results

Herein, we present a bioinformatics tool, CompGO, for identifying Differentially Enriched Gene Ontologies, called DiEGOs, and pathways, through the use of a z-score derivation of log odds ratios, and visualizing these differences at GO and pathway level. Through public experimental data focused on the cardiac transcription factor NKX2-5, we illustrate the problems associated with comparing GO enrichments between experiments using a simple overlap approach.

Conclusions

SUBMITTER: Waardenberg AJ 

PROVIDER: S-EPMC4557902 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature