Speaker
Description
The identification of overrepresented Gene Ontology (GO) terms in a set of genes is a standard approach to obtain functional associations, e.g. to characterize the set of differentially expressed genes between treatment and control samples. Here, we present the R package GO-a-GO that annotates Gene Ontology terms that are enriched in a given set of gene pairs. This provides the opportunity to annotate which functions are associated with gene pairs defined by a selected group of chromatin contacts, such as differential contacts between cell types or chromatin loops.
GO-a-GO calculates enrichment from a permutation test for overrepresentation of gene pairs that are associated with a shared GO term. Such gene pairs are counted for the original set of gene pairs and compared against randomized sets in which the structure of the pairs is preserved, but the gene identities (including the associated GO terms) are permuted. Therefore, we do not focus on the fact that the term is enriched in a group of genes, but that genes with this term get paired more often than expected.
We used GO-a-GO to identify GO terms enriched in gene pairs associated with human chromatin loops, revealing several enriched functional terms that were not enriched when annotating the gene set without the information on gene pairs. In summary, we developed a package to study the function of chromatin contacts, which integrates with the Bioconductor ecosystem and can be used independently on the type of experimental method used and the nature of contacts.
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Additional Material or Paper
Package submitted to Bioconductor, public GitHub repository: https://github.com/ajank/GOaGO
| Keywords: Please list up to 5 keywords to help us find the right session for your contribution. | bioinformatics, computational biology, Bioconductor, Gene Ontology |
|---|---|
| Virtual Option | This submission is for onsite presentation only |
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| The author(s) agree(s) to take responsibility and be accountable for the contents of the submission and is/are authorized to present it. | Confirm |