Waardenberg, Ashley J and Basset, Samuel D and Bouveret, Romaric and Harvey, Richard P (2015) CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments. BMC Bioinformatics, 16. p. 275. ISSN 1471-2105 (Gold OA)
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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
We have developed an R/Bioconductor package, CompGO, which implements a new statistic normally used in epidemiological studies for performing comparative GO analyses and visualizing comparisons from . BED data containing genomic coordinates as well as gene lists as inputs. We justify the statistic through inclusion of experimental data and compare to the commonly used overlap method. CompGO is freely available as a R/Bioconductor package enabling easy integration into existing pipelines and is available at: http://www.bioconductor.org/packages/release/bioc/html/CompGO.html packages/release/bioc/html/CompGO.html.
(NHMRC grants 573705, 573703, 1061539), ARC Strategic Initiative in Stem Cell Science (Stem Cells Australia; 110001002), the Australian-India Strategic Research Fund (BF020084) and Foundation Leducq).
| Item Type: | Article |
|---|---|
| Subjects: | R Medicine > R Medicine (General) |
| Depositing User: | Repository Administrator |
| Date Deposited: | 22 Jan 2016 00:20 |
| Last Modified: | 28 Sep 2016 05:39 |
| URI: | https://eprints.victorchang.edu.au/id/eprint/222 |
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