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Open Access Research article

Functional divergence of gene duplicates – a domain-centric view

Mugdha Khaladkar1 and Sridhar Hannenhalli2*

Author Affiliations

1 Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA

2 University of Maryland, 3104G Biomolecular Sciences Building (#296), College Park, MD, USA

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BMC Evolutionary Biology 2012, 12:126  doi:10.1186/1471-2148-12-126

Published: 27 July 2012

Additional files

Additional file 1:

Table S1. Number and percentage of paralogs deemed to be asymmetrically evolving (FDR = 5 %) based on the whole protein and using Fisher Exact test (FET). Table S2. Number and percentage of paralogs deemed to be asymmetrically evolving (FDR = 0.01 %) based on the whole protein and using Fisher Exact test (FET). Table S3. Fisher exact test based analysis of asymmetrically evolving duplicate gene pairs using sampled codons to create artificial domains. Table S4. Number and percentage of paralogs deemed to be asymmetrically evolving (FDR = 10 %) based on the non-domain linker regions using Fisher Exact test (FET). Table S5. Duplicate gene pairs that contained multiple asymmetrically evolving domains categorized based on whether all the faster domains were in the same copy (Category 1) or distributed between the two copies (Category 2). Table S6. Frequency of occurrence of each of the protein domains and the fraction of times they were detected to be evolving asymmetrically (FET P-value < = 0.05, FDR < = 20 %). Supplementary Results. Differing regions of the gene duplicates are targeted for non-synonymous substitutions.

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