Using Protein Domains to Identify Pathways in Gene Lists
Author Information
Author(s): Hahne Florian, Mehrle Alexander, Arlt Dorit, Poustka Annemarie, Wiemann Stefan, Beissbarth Tim
Primary Institution: German Cancer Research Center
Hypothesis
Protein domains can be treated as functional elements of the proteins, the set of interpro-domains of the proteins of one pathway could serve as its functional fingerprint.
Conclusion
The study demonstrates that domain-based pathway enrichment analysis is a sensitive method for testing pathway enrichment in sparsely annotated gene lists.
Supporting Evidence
- The method can recover pathway memberships based on simulated gene lists with high accuracy.
- An R-based software package called domainsignatures is available for performing this analysis.
- The approach was validated using both simulation studies and real biological datasets.
Takeaway
This study shows how scientists can use information about protein domains to figure out which biological pathways are important for certain genes, even when those genes don't have much information available.
Methodology
The study involved a simulation study using the KEGG database to validate the approach of comparing protein domain signatures of gene lists with known pathways.
Limitations
Some pathways could not be classified well, particularly small metabolic pathways or those with very few proteins.
Digital Object Identifier (DOI)
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