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dc.contributor.authorZhou, Naihui
dc.contributor.authorJiang, Yuxiang
dc.contributor.authorBergquist, Timothy R.
dc.contributor.authorLee, Alexandra J.
dc.contributor.authorKacsoh, Balint Z.
dc.contributor.authorCrocker, Alex W.
dc.contributor.authorLewis, Kimberley A.
dc.contributor.authorGeorghiou, George
dc.contributor.authorNguyen, Huy N.
dc.contributor.authorHamid, Md Nafiz
dc.contributor.authorDavis, Larry
dc.contributor.authorDogan, Tunca
dc.contributor.authorAtalay, Volkan
dc.contributor.authorRifaioglu, Ahmet S.
dc.contributor.authorDalkıran, Alperen
dc.contributor.authorCetin Atalay, Rengul
dc.contributor.authorZhang, Chengxin
dc.contributor.authorHurto, Rebecca L.
dc.contributor.authorFreddolino, Peter L.
dc.contributor.authorZhang, Yang
dc.contributor.authorBhat, Prajwal
dc.contributor.authorSupek, Fran
dc.contributor.authorFernández, José M.
dc.contributor.authorGemovic, Branislava
dc.contributor.authorPerovic, Vladimir R.
dc.contributor.authorDavidović, Radoslav S.
dc.contributor.authorSumonja, Neven
dc.contributor.authorVeljkovic, Nevena
dc.contributor.authorAsgari, Ehsaneddin
dc.contributor.authorMofrad, Mohammad R.K.
dc.contributor.authorProfiti, Giuseppe
dc.contributor.authorSavojardo, Castrense
dc.contributor.authorMartelli, Pier Luigi
dc.contributor.authorCasadio, Rita
dc.contributor.authorBoecker, Florian
dc.contributor.authorSchoof, Heiko
dc.contributor.authorKahanda, Indika
dc.contributor.authorThurlby, Natalie
dc.contributor.authorMcHardy, Alice C.
dc.contributor.authorRenaux, Alexandre
dc.contributor.authorSaidi, Rabie
dc.contributor.authorGough, Julian
dc.contributor.authorFreitas, Alex A.
dc.contributor.authorAntczak, Magdalena
dc.contributor.authorFabris, Fabio
dc.contributor.authorWass, Mark N.
dc.contributor.authorHou, Jie
dc.contributor.authorCheng, Jianlin
dc.contributor.authorWang, Zheng
dc.contributor.authorRomero, Alfonso E.
dc.contributor.authorPaccanaro, Alberto
dc.contributor.authorYang, Haixuan
dc.contributor.authorGoldberg, Tatyana
dc.contributor.authorZhao, Chenguang
dc.contributor.authorHolm, Liisa
dc.contributor.authorTörönen, Petri
dc.contributor.authorMedlar, Alan J.
dc.contributor.authorZosa, Elaine
dc.contributor.authorBorukhov, Itamar
dc.contributor.authorNovikov, Ilya
dc.contributor.authorWilkins, Angela
dc.contributor.authorLichtarge, Olivier
dc.contributor.authorChi, Po-Han
dc.contributor.authorTseng, Wei-Cheng
dc.contributor.authorLinial, Michal
dc.contributor.authorRose, Peter W.
dc.contributor.authorDessimoz, Christophe
dc.contributor.authorVidulin, Vedrana
dc.contributor.authorDzeroski, Saso
dc.contributor.authorSillitoe, Ian
dc.contributor.authorDas, Sayoni
dc.contributor.authorLees, Jonathan Gill
dc.contributor.authorJones, David T.
dc.contributor.authorWan, Cen
dc.contributor.authorCozzetto, Domenico
dc.contributor.authorFa, Rui
dc.contributor.authorTorres, Mateo
dc.contributor.authorWarwick Vesztrocy, Alex
dc.contributor.authorRodriguez, Jose Manuel
dc.contributor.authorTress, Michael L.
dc.contributor.authorFrasca, Marco
dc.contributor.authorNotaro, Marco
dc.contributor.authorGrossi, Giuliano
dc.contributor.authorPetrini, Alessandro
dc.contributor.authorRe, Matteo
dc.contributor.authorValentini, Giorgio
dc.contributor.authorMesiti, Marco
dc.contributor.authorRoche, Daniel B.
dc.contributor.authorReeb, Jonas
dc.contributor.authorRitchie, David W.
dc.contributor.authorAridhi, Sabeur
dc.contributor.authorAlborzi, Seyed Ziaeddin
dc.contributor.authorDevignes, Marie-Dominique
dc.contributor.authorKoo, Da Chen Emily
dc.contributor.authorBonneau, Richard
dc.contributor.authorGligorijević, Vladimir
dc.contributor.authorBarot, Meet
dc.contributor.authorFang, Hai
dc.contributor.authorToppo, Stefano
dc.contributor.authorLavezzo, Enrico
dc.contributor.authorFalda, Marco
dc.contributor.authorBerselli, Michele
dc.contributor.authorTosatto, Silvio C.E.
dc.contributor.authorCarraro, Marco
dc.contributor.authorPiovesan, Damiano
dc.contributor.authorUr Rehman, Hafeez
dc.contributor.authorMao, Qizhong
dc.contributor.authorZhang, Shanshan
dc.contributor.authorVucetic, Slobodan
dc.contributor.authorBlack, Gage S.
dc.contributor.authorJo, Dane
dc.contributor.authorSuh, Erica
dc.contributor.authorDayton, Jonathan B.
dc.contributor.authorLarsen, Dallas J.
dc.contributor.authorOmdahl, Ashton R.
dc.contributor.authorMcGuffin, Liam J.
dc.contributor.authorBrackenridge, Danielle A.
dc.contributor.authorBabbitt, Patricia C.
dc.contributor.authorYunes, Jeffrey M.
dc.contributor.authorFontana, Paolo
dc.contributor.authorZhang, Feng
dc.contributor.authorZhu, Shanfeng
dc.contributor.authorYou, Ronghui
dc.contributor.authorZhang, Zihan
dc.contributor.authorDai, Suyang
dc.contributor.authorYao, Shuwei
dc.contributor.authorTian, Weidong
dc.contributor.authorCao, Renzhi
dc.contributor.authorChandler, Caleb
dc.contributor.authorAmezola, Miguel
dc.contributor.authorJohnson, Devon
dc.contributor.authorChang, Jia-Ming
dc.contributor.authorLiao, Wen-Hung
dc.contributor.authorLiu, Yi-Wei
dc.contributor.authorPascarelli, Stefano
dc.contributor.authorFrank, Yotam
dc.contributor.authorHoehndorf, Robert
dc.contributor.authorKulmanov, Maxat
dc.contributor.authorBoudellioua, Imene
dc.contributor.authorPolitano, Gianfranco
dc.contributor.authorDi Carlo, Stefano
dc.contributor.authorBenso, Alfredo
dc.contributor.authorHakala, Kai
dc.contributor.authorGinter, Filip
dc.contributor.authorMehryary, Farrokh
dc.contributor.authorKaewphan, Suwisa
dc.contributor.authorBjörne, Jari
dc.contributor.authorMoen, Hans
dc.contributor.authorTolvanen, Martti E.E.
dc.contributor.authorSalakoski, Tapio
dc.contributor.authorKihara, Daisuke
dc.contributor.authorJain, Aashish
dc.contributor.authorŠmuc, Tomislav
dc.contributor.authorAltenhoff, Adrian
dc.contributor.authorBen-Hur, Asa
dc.contributor.authorRost, Burkhard
dc.contributor.authorBrenner, Steven E.
dc.contributor.authorOrengo, Christine A.
dc.contributor.authorJeffery, Constance J.
dc.contributor.authorBosco, Giovanni
dc.contributor.authorHogan, Deborah A.
dc.contributor.authorMartin, Maria J.
dc.contributor.authorO’Donovan, Claire
dc.contributor.authorMooney, Sean D.
dc.contributor.authorGreene, Casey S.
dc.contributor.authorRadivojac, Predrag
dc.contributor.authorFriedberg, Iddo
dc.date.accessioned2020-09-15T13:16:59Z
dc.date.available2020-09-15T13:16:59Z
dc.date.issued2019
dc.identifier.citationNaihui Zhou, Yuxiang Jiang, Bergquist, T., Lee, A., Balint Kacsoh, Crocker, A., Lewis, K., Georghiou, G., Nguyen, H., Md Nafiz Hamid, Davis, L., Tunca Dogan, Atalay, V., Rifaioglu, A., Dalkıran, A., Rengul Cetin Atalay, Chengxin Zhang, Hurto, R., Freddolino, P., … Friedberg, I. (2019). The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. figshare. https://doi.org/10.6084/M9.FIGSHARE.C.4745834
dc.identifier.doi10.6084/m9.figshare.c.4745834
dc.identifier.urihttp://hdl.handle.net/10754/665161
dc.description.abstractAbstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results 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 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. Conclusion 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 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.
dc.publisherfigshare
dc.subjectGenetics
dc.subjectFOS: Biological sciences
dc.subjectMolecular Biology
dc.subject69999 Biological Sciences not elsewhere classified
dc.subject80699 Information Systems not elsewhere classified
dc.subjectFOS: Computer and information sciences
dc.subject111714 Mental Health
dc.subjectFOS: Health sciences
dc.titleThe CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
dc.typeDataset
dc.contributor.departmentBio-Ontology Research Group (BORG)
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.institutionVeterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.
dc.contributor.institutionIndiana University Bloomington, Bloomington, Indiana, USA.
dc.contributor.institutionEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.
dc.contributor.institutionProgram in Bioinformatics and Computational Biology, Ames, IA, USA.
dc.contributor.institutionDepartment of Computer Engineering, Hacettepe University, Ankara, Turkey.
dc.contributor.institutionDepartment of Computer Engineering, Middle East Technical University (METU), Ankara, Turkey.
dc.contributor.institutionCanSyL, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.
dc.contributor.institutionDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
dc.contributor.institutionAchira Labs, Bangalore, India.
dc.contributor.institutionInstitute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
dc.contributor.institutionLaboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences VINCA, University of Belgrade, Belgrade, Serbia.
dc.contributor.institutionMolecular Cell Biomechanics Laboratory, Departments of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
dc.contributor.institutionBologna Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
dc.contributor.institutionUniversity of Bonn: INRES Crop Bioinformatics, Bonn, North Rhine-Westphalia, Germany.
dc.contributor.institutionINRES Crop Bioinformatics, University of Bonn, Bonn, Germany.
dc.contributor.institutionGianforte School of Computing, Montana State University, Bozeman, Montana, USA.
dc.contributor.institutionUniversity of Bristol, Computer Science, Bristol, Bristol, United Kingdom.
dc.contributor.institutionInteruniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium.
dc.contributor.institutionEuropean Molecular Biolo gy Labora tory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
dc.contributor.institutionMRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
dc.contributor.institutionSchool of Biosciences, University of Kent, Canterbury, Kent, United Kingdom.
dc.contributor.institutionUniversity of Kent, School of Computing, Canterbury, United Kingdom.
dc.contributor.institutionUniversity of Missouri, Computer Science, Columbia, Missouri, USA.
dc.contributor.institutionDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
dc.contributor.institutionUniversity of Miami, Coral Gables, Florida, USA.
dc.contributor.institutionCentre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom.
dc.contributor.institutionSchool of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Galway, Ireland.
dc.contributor.institutionDepartment of Informatics, Bioinformatics & Computational Biology-i12, Technische Universitat Munchen, Munich, Germany.
dc.contributor.institutionFaculty for Informatics, Garching, Germany.
dc.contributor.institutionInstitute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Finland, Helsinki, Finland.
dc.contributor.institutionInstitute of Biotechnology, University of Helsinki, Helsinki, Finland.
dc.contributor.institutionCompugen Ltd., Holon, Israel.
dc.contributor.institutionBaylor College of Medicine, Department of Biochemistry and Molecular Biology, Houston, TX, USA.
dc.contributor.institutionBaylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, USA.
dc.contributor.institutionNational TsingHua University, Hsinchu, Taiwan.
dc.contributor.institutionDepartment of Electrical Engineering in National Tsing Hua University, Hsinchu City, Taiwan.
dc.contributor.institutionThe Hebrew University of Jerusalem, Jerusalem, Israel.
dc.contributor.institutionDepartment of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
dc.contributor.institutionDepartment of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia.
dc.contributor.institutionJozef Stefan Institute, Ljubljana, Slovenia.
dc.contributor.institutionResearch Department of Structural and Molecular Biology, University College London, London, England.
dc.contributor.institutionResearch Department of Structural and Molecular Biology, University College London, London, United Kingdom.
dc.contributor.institutionDepartment of Computer Science, University College London, London, United Kingdom.
dc.contributor.institutionDepartment of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
dc.contributor.institutionCardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
dc.contributor.institutionUniversità degli Studi di Milano - Computer Science Department - AnacletoLab, Milan, Milan, Italy.
dc.contributor.institutionDepartment of Informatics, Bioinformatics and Computational Biology-i12, Technische Universitat Munchen, Munich, Germany.
dc.contributor.institutionUniversity of Lorraine, CNRS, Inria, LORIA, Nancy, 54000, France.
dc.contributor.institutionDepartment of Biology, New York University, New York, NY, USA.
dc.contributor.institutionNYU Center for Data Science, New York, 10010, NY, USA.
dc.contributor.institutionCenter for Computational Biology (CCB), Flatiron Institute, Simons Foundation, New York, New York, USA.
dc.contributor.institutionCenter for Data Science, New York University, New York, 10011, NY, USA.
dc.contributor.institutionWellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
dc.contributor.institutionDepartment of Molecular Medicine, University of Padova, Padova, Italy.
dc.contributor.institutionDepartment of Biology, University of Padova, Padova, Italy.
dc.contributor.institutionDepartment of Biomedical Sciences, University of Padua, Padova, Italy.
dc.contributor.institutionDepartment of Computer Science, National University of Computer and Emerging Sciences, Peshawar, Khyber Pakhtoonkhwa, Pakistan.
dc.contributor.institutionDepartment of Computer and Information Sciences, Temple University, Philadelphia, PA, USA.
dc.contributor.institutionDepartment of Biology, Brigham Young University, Provo, UT, USA.
dc.contributor.institutionResearch and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy.
dc.contributor.institutionState Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, Shanghai, China.
dc.contributor.institutionSchool of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.
dc.contributor.institutionState Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, Shanghai, China.
dc.contributor.institutionDepartment of Computer Science, Pacific Lutheran University, Tacoma, WA, USA.
dc.contributor.institutionDepartment of Computer Science, National Chengchi University, Taipei, Taiwan.
dc.contributor.institutionOkinawa Institute of Science and Technology, Tancha, Okinawa, Japan.
dc.contributor.institutionTel Aviv University, Tel Aviv, Israel.
dc.contributor.institutionControl and Computer Engineering Department, Politecnico di Torino, Torino, TO, Italy.
dc.contributor.institutionDepartment of Future Technologies, Turku NLP Group, University of Turku, Turku, Finland.
dc.contributor.institutionDepartment of Future Technologies, Faculty of Science and Engineering, University of Turku, Turku, FI-20014, Finland.
dc.contributor.institutionUniversity of Turku, Turku, Finland.
dc.contributor.institutionDepartment of Biological Sciences, Department of Computer Science, Purdue University, 47907, IN, USA.
dc.contributor.institutionDepartment of Computer Science, Purdue University, West Lafayette, IN, USA.
dc.contributor.institutionDivision of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia.
dc.contributor.institutionDepartment of Computer Science, ETH Zurich, Zurich, Switzerland.
dc.contributor.institutionDepartment of Computer Science, Colorado State University, Fort Collins, CO, USA.
dc.contributor.institutionDepartment of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
dc.contributor.institutionKhoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
kaust.personHoehndorf, Robert
kaust.personKulmanov, Maxat
kaust.personBoudellioua, Imene
dc.relation.issupplementtoDOI:10.1186/s13059-019-1835-8
display.relations<b> Is Supplement To:</b><br/> <ul> <li><i>[Article]</i> <br/> Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., … Hamid, M. N. (2019). The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20(1). doi:10.1186/s13059-019-1835-8. DOI: <a href="https://doi.org/10.1186/s13059-019-1835-8" >10.1186/s13059-019-1835-8</a> HANDLE: <a href="http://hdl.handle.net/10754/660434">10754/660434</a></li></ul>


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