The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
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CAFA 挑战报告通过实验筛选改进了蛋白质功能预测和数百个基因的新功能注释
DOI：
10.1101/653105
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Zhou N
中科院分区：
文献类型：
--
作者：
Zhou N
BackgroundThe Critical Assessment of Functional Annotation（CAFA）是一个持续的，全球性的，社区驱动的努力，以评估和提高计算注释的蛋白质function.ResultsHere，我们报告的结果的第三个CAFA挑战，CAFA 3，功能扩展分析在以前的CAFA轮，无论是在分析的数据量和分析的类型进行。在一个新的和主要的新发展中，计算预测和评估目标驱动了一些实验测定，导致了1000多个基因的新功能注释。具体而言，我们在白色念珠菌和金黄色假单胞菌基因组中进行了实验性全基因组突变筛查，这为我们提供了与生物膜形成和运动相关的基因的全基因组实验数据。我们进一步选择基因inDrosophila melanogaster，我们怀疑参与长期memory.ConclusionWe的结论是，虽然预测的分子功能和生物过程的注释略有改善，随着时间的推移，那些细胞成分没有。以术语为中心的实验注释预测仍然同样具有挑战性;尽管顶级方法的性能明显优于C中基线方法的预期。albicanandD.黑腹，它留下了相当大的空间和需要改进。最后，我们报告说，CAFA社区现在涉及广泛的参与者，他们具有生物信息学，生物实验，生物定位和生物本体学方面的专业知识，共同努力改善功能注释，计算功能预测以及我们在大型实验屏幕时代管理大数据的能力。
BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, 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 inCandida albicansandPseudomonas aureginosagenomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes inDrosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe 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 inC. albicansandD. melanogaster, 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.
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影响因子：
3
作者：
Bernardo, Stella M.;Khalique, Zachary;Lee, Samuel A.
通讯作者：
Lee, Samuel A.
影响因子：
2.9
作者：
Clark, Wyatt T.;Radivojac, Predrag
通讯作者：
Radivojac, Predrag
DOI：
10.1007/978-1-4939-3743-1_5
发表时间：
2017-01-01
期刊：
GENE ONTOLOGY HANDBOOK
影响因子：
--
作者：
Cozzetto, Domenico;Jones, David T.
通讯作者：
Jones, David T.
影响因子：
4.5
作者：
Ventura M;Turroni F;Zomer A;Foroni E;Giubellini V;Bottacini F;Canchaya C;Claesson MJ;He F;Mantzourani M;Mulas L;Ferrarini A;Gao B;Delledonne M;Henrissat B;Coutinho P;Oggioni M;Gupta RS;Zhang Z;Beighton D;Fitzgerald GF;O'Toole PW;van Sinderen D
通讯作者：
van Sinderen D
影响因子：
14.9
作者：
Szklarczyk D;Franceschini A;Wyder S;Forslund K;Heller D;Huerta-Cepas J;Simonovic M;Roth A;Santos A;Tsafou KP;Kuhn M;Bork P;Jensen LJ;von Mering C
通讯作者：
von Mering C