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bioRxiv · 10.1101/042036

Towards Consensus Gene Ages

Benjamin J. Liebeskind·Claire D. McWhite·Edward M. Marcotte
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Abstract

Correctly estimating the age of a gene or gene family is important for a variety of fields, including molecular evolution, comparative genomics, and phylogenetics, and increasingly for systems biology and disease genetics. However, most studies use only a point estimate of a genes age, neglecting the substantial uncertainty involved in this estimation. Here, we characterize this uncertainty by investigating the effect of algorithm choice on gene-age inference and calculate consensus gene ages with attendant error distributions for a variety of model eukaryotes. We use thirteen orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis. Systematic error was found to be a large factor in estimating gene age, suggesting that simple consensus algorithms are not enough to give a reliable point estimate. We also found that different sources of error can affect downstream analyses, such as gene ontology enrichment. Our consensus gene-age datasets, with associated error terms, are made fully available at so that researchers can propagate this uncertainty through their analyses (https://github.com/marcottelab/Gene-Ages).

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Benjamin J. Liebeskind, Claire D. McWhite, Edward M. Marcotte. 2016-03-01. Towards Consensus Gene Ages. https://doi.org/10.1101/042036

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