ArticleGenome biology2019
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
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Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 264 papers.
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167 authors at 20 institutions in 20 countries.
Naihui ZhouVeterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
Yuxiang JiangIndiana University Bloomington, Bloomington, Indiana, USA.
Timothy R BergquistDepartment of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
Alexandra J LeeDepartment of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.
Balint Z KacsohGeisel School of Medicine at Dartmouth, Hanover, NH, USA.
Alex W CrockerDepartment of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
Kimberley A LewisDepartment of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
George GeorghiouEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.
Huy N NguyenVeterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
Md Nafiz HamidVeterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
Larry DavisProgram in Bioinformatics and Computational Biology, Ames, IA, USA.
Tunca DoganDepartment of Computer Engineering, Hacettepe University, Ankara, Turkey.
Volkan AtalayDepartment of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.
Ahmet S RifaiogluDepartment of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.
Alperen DalkıranDepartment of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.
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Chengxin ZhangDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Rebecca L HurtoDepartment of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
Peter L FreddolinoDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Yang ZhangDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Prajwal BhatAchira Labs, Bangalore, India.
Fran SupekInstitute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
José M FernándezINB Coordination Unit, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain.
Branislava GemovicLaboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia.
Vladimir R PerovicLaboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia.
Radoslav S DavidovićLaboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia.
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Pier Luigi MartelliBologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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Alice C McHardyComputational Biology of Infection Research, Helmholtz Centre for Infection Research, Brunswick, Germany.
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Alfonso E RomeroCentre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom.
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Po-Han ChiNational TsingHua University, Hsinchu, Taiwan.
Wei-Cheng TsengDepartment of Electrical Engineering in National Tsing Hua University, Hsinchu City, Taiwan.
Michal LinialThe Hebrew University of Jerusalem, Jerusalem, Israel.
Peter W RoseUniversity of California San Diego, San Diego Supercomputer Center, La Jolla, California, USA.
Christophe DessimozDepartment of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
Vedrana VidulinDepartment of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia.
Saso DzeroskiJozef Stefan Institute, Ljubljana, Slovenia.
Ian SillitoeResearch Department of Structural and Molecular Biology, University College London, London, England.
Sayoni DasResearch Department of Structural and Molecular Biology, University College London, London, United Kingdom.
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Burkhard RostDepartment of Informatics, Bioinformatics & Computational Biology-i12, Technische Universitat Munchen, Munich, Germany.
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Christine A OrengoResearch Department of Structural and Molecular Biology, University College London, London, United Kingdom.
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Funding
Transform Dissemination and Implementation Science in CTSA ProgramsUL1TR002319 · NCATS · UNIVERSITY OF WASHINGTON · PI John K. Amory · 2017 to 2026
$100.0MCD2H - The National COVID Cohort Collaborative (N3C) IDeA CTR CollaborationU24TR002306 · NCATS · UNIVERSITY OF COLORADO DENVER · PI CHUTE, CHRISTOPHER G, EICHMANN, DAVID A. · 2017 to 2021
$28.9MUnderstanding the role of RNA-binding protein mutations in cancerP20GM113132 · NIGMS · DARTMOUTH COLLEGE · PI MADDEN, DEAN R · 2016 to 2025
$25.9MGENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MIntegrated Prediction of Protein Struture at 1D, 2D and 3D LevelsR01GM093123 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2010 to 2023
$3.8MBuilding a unified framework for understanding bacterial gene regulation and chromosomal architectureR35GM128637 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Lydia Petra Freddolino · 2018 to 2026
$3.6MCompressive Structural BioInformatics: High Efficiency 3D Structure CompressionU01CA198942 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ROSE, PETER W · 2015 to 2017
$1.6MProtein function prediction by statistical phylogenomicsR01GM071749 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI BRENNER, STEVEN E · 2007 to 2010
$1.4MStructural Modeling of Multifarious Protein ComplexesR01GM123055 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2017 to 2020
$1.2MGenome-wide measurement of bacterial transcriptional regulatory statesR00GM097033 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI FREDDOLINO, LYDIA PETRA · 2015 to 2017
$746kMeasure and Classify the Structure and Function of Genome Topological DomainsR15GM120650 · NIGMS · UNIVERSITY OF SOUTHERN MISSISSIPPI · PI SUNG, ANDREW H. · 2016 to 2016
$444kComputationally Designed Stable Artificial Phosphotriesterases for Detoxification of Organophosphorus AgentsR21NS103831 · NINDS · NEW YORK UNIVERSITY · PI MONTCLARE, JIN KIM · 2017 to 2018
$349kBiotechnology and Biological Sciences Research Council BB/F00964X/1Biotechnology and Biological Sciences Research Council BB/K004131/1Biotechnology and Biological Sciences Research Council BB/L002817/1Biotechnology and Biological Sciences Research Council BB/L020505/1Biotechnology and Biological Sciences Research Council BB/M015009/1Biotechnology and Biological Sciences Research Council BB/M025047/1Biotechnology and Biological Sciences Research Council BB/N004876/1Biotechnology and Biological Sciences Research Council BB/N019431/1Medical Research Council MC_UP_1201/14NCATS NIH HHS U24 TR002306NCATS NIH HHS UL1 TR002319NCI NIH HHS U01 CA198942NHGRI NIH HHS U41 HG007234NIGMS NIH HHS P20 GM113132NIGMS NIH HHS R00 GM097033NIGMS NIH HHS R01 GM071749NIGMS NIH HHS R01 GM093123NIGMS NIH HHS R01 GM123055NIGMS NIH HHS R15 GM120650NIGMS NIH HHS R35 GM128637NINDS NIH HHS R21 NS103831
Abstract
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 in Candida albicans and Pseudomonas aureginosa 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 Drosophila 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 in C. albicans and D. 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.
Indexed as
AnimalsBiofilmsCandida albicansDrosophila melanogasterGenome, BacterialGenome, FungalHumansLocomotionMemory, Long-TermMolecular Sequence AnnotationPseudomonas aeruginosaBiofilmCommunity challengeCritical assessmentLong-term memoryProtein function prediction
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