The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

DOI DOI HANDLE HANDLE HANDLE ほか14件をすべて表示 一部だけ表示 研究データあり 被引用文献3件 参考文献1件 オープンアクセス

説明

<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in <jats:italic>Candida albicans</jats:italic> and <jats:italic>Pseudomonas aureginosa</jats:italic> genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in <jats:italic>Drosophila melanogaster</jats:italic>, which we suspected of being involved in long-term memory.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusion</jats:title> <jats:p>We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in <jats:italic>C. albicans</jats:italic> and <jats:italic>D. melanogaster</jats:italic>, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</jats:p> </jats:sec>

収録刊行物

  • Genome Biology

    Genome Biology 20 (1), 244-, 2019-11-19

    Springer Science and Business Media LLC

被引用文献 (3)*注記

もっと見る

参考文献 (1)*注記

もっと見る

関連論文

もっと見る

キーワード

問題の指摘

ページトップへ