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

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العنوان: The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
المؤلفون: Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R., Lee, Alexandra J., Kacsoh, Balint Z., Crocker, Alex W., Lewis, Kimberley A., Georghiou, George, Nguyen, Huy N., Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S., Dalkiran, Alperen, Atalay, Rengul Cetin, Zhang, Chengxin, Hurto, Rebecca L., Freddolino, Peter L., Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernandez, Jose M., Gemovic, Branislava, Perovic, Vladimir R., Davidovic, Radoslav S., Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad R. K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C., Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A., Antczak, Magdalena, Fabris, Fabio, Wass, Mark N., Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E., Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J., Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W., Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T., Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Vesztrocy, Alex Warwick, Rodriguez, Jose Manuel, Tress, Michael L., Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B., Reeb, Jonas, Ritchie, David W., Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijevic, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C. E., Carraro, Marco, Piovesan, Damiano, Rehman, Hafeez Ur, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S., Jo, Dane, Suh, Erica, Dayton, Jonathan B., Larsen, Dallas J., Omdahl, Ashton R., McGuffin, Liam J., Brackenridge, Danielle A., Babbitt, Patricia C., Yunes, Jeffrey M., Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Bjorne, Jari, Moen, Hans, Tolvanen, Martti E. E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Smuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E., Orengo, Christine A., Jeffery, Constance J., Bosco, Giovanni, Hogan, Deborah A., Martin, Maria J., O'Donovan, Claire, Mooney, Sean D., Greene, Casey S., Radivojac, Predrag, Friedberg, Iddo
المساهمون: Computational genomics, Institute of Biotechnology, Bioinformatics, Genetics, Helsinki Institute of Life Science HiLIFE, Discovery Research Group/Prof. Hannu Toivonen
بيانات النشر: BioMed Central Ltd
سنة النشر: 2020
المجموعة: Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto
مصطلحات موضوعية: Protein function prediction, Long-term memory, Biofilm, Critical assessment, Community challenge, CANDIDA-ALBICANS, ONTOLOGY, IDENTIFICATION, GENERATION, LIBRARY, 318 Medical biotechnology
الوصف: 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. ; Peer reviewed
نوع الوثيقة: article in journal/newspaper
وصف الملف: application/pdf
اللغة: English
العلاقة: The work of IF was funded, in part, by the National Science Foundation award DBI-1458359. The work of CSG and AJL was funded, in part, by the National Science Foundation award DBI-1458390 and GBMF 4552 from the Gordon and Betty Moore Foundation. The work of DAH and KAL was funded, in part, by the National Science Foundation award DBI-1458390, National Institutes of Health NIGMS P20 GM113132, and the Cystic Fibrosis Foundation CFRDP STANTO19R0. The work of AP, HY, AR, and MT was funded by BBSRC grants BB/K004131/1, BB/F00964X/1 and BB/M025047/1, Consejo Nacional de Ciencia y Tecnologia Paraguay (CONACyT) grants 14-INV-088 and PINV15-315, and NSF Advances in BioInformatics grant 1660648. The work of JC was partially supported by an NIH grant (R01GM093123) and two NSF grants (DBI 1759934 and IIS1763246). ACM acknowledges the support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy -EXC 2155 "RESIST" - Project ID 39087428. DK acknowledges the support from the National Institutes of Health (R01GM123055) and the National Science Foundation (DMS1614777, CMMI1825941). PB acknowledges the support from the National Institutes of Health (R01GM60595). GB and BZK acknowledge the support from the National Science Foundation (NSF 1458390) and NIH DP1MH110234. FS was funded by the ERC StG 757700 "HYPER-INSIGHT" and by the Spanish Ministry of Science, Innovation and Universities grant BFU2017-89833-P. FS further acknowledges the funding from the Severo Ochoa award to the IRB Barcelona. TS was funded by the Centre of Excellence project "BioProspecting of Adriatic Sea", co-financed by the Croatian Government and the European Regional Development Fund (KK.01.1.1.01.0002). The work of SK was funded by ATT Tieto kayttoon grant and Academy of Finland. JB and HM acknowledge the support of the University of Turku, the Academy of Finland and CSC -IT Center for Science Ltd. TB and SM were funded by the NIH awards UL1 TR002319 and U24 TR002306. The work of CZ and ZW was funded by the National Institutes of Health R15GM120650 to ZW and start-up funding from the University of Miami to ZW. The work of PWR was supported by the National Cancer Institute of the National Institutes of Health under Award Number U01CA198942. PR acknowledges NSF grant DBI-1458477. PT acknowledges the support from Helsinki Institute for Life Sciences. The work of AJM was funded by the Academy of Finland (No. 292589). The work of FZ and WT was funded by the National Natural Science Foundation of China (31671367, 31471245, 91631301) and the National Key Research and Development Program of China (2016YFC1000505, 2017YFC0908402]. CS acknowledges the support by the Italian Ministry of Education, University and Research (MIUR) PRIN 2017 project 2017483NH8. SZ is supported by the National Natural Science Foundation of China (No. 61872094 and No. 61572139) and Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01). PLF and RLH were supported by the National Institutes of Health NIH R35-GM128637 and R00-GM097033. JG, DTJ, CW, DC, and RF were supported by the UK Biotechnology and Biological Sciences Research Council (BB/N019431/1, BB/L020505/1, and BB/L002817/1) and Elsevier. The work of YZ and CZ was funded in part by the National Institutes of Health award GM083107, GM116960, and AI134678; the National Science Foundation award DBI1564756; and the Extreme Science and Engineering Discovery Environment (XSEDE) award MCB160101 and MCB160124.; Zhou , N , Jiang , Y , Bergquist , T R , Lee , A J , Kacsoh , B Z , Crocker , A W , Lewis , K A , Georghiou , G , Nguyen , H N , Hamid , M N , Davis , L , Dogan , T , Atalay , V , Rifaioglu , A S , Dalkiran , A , Atalay , R C , Zhang , C , Hurto , R L , Freddolino , P L , Zhang , Y , Bhat , P , Supek , F , Fernandez , J M , Gemovic , B , Perovic , V R , Davidovic , R S , Sumonja , N , Veljkovic , N , Asgari , E , Mofrad , M R K , Profiti , G , Savojardo , C , Martelli , P L , Casadio , R , Boecker , F , Schoof , H , Kahanda , I , Thurlby , N , McHardy , A C , Renaux , A , Saidi , R , Gough , J , Freitas , A A , Antczak , M , Fabris , F , Wass , M N , Hou , J , Cheng , J , Wang , Z , Romero , A E , Paccanaro , A , Yang , H , Goldberg , T , Zhao , C , Holm , L , Törönen , P , Medlar , A J , Zosa , E , Borukhov , I , Novikov , I , Wilkins , A , Lichtarge , O , Chi , P-H , Tseng , W-C , Linial , M , Rose , P W , Dessimoz , C , Vidulin , V , Dzeroski , S , Sillitoe , I , Das , S , Lees , J G , Jones , D T , Wan , C , Cozzetto , D , Fa , R , Torres , M , Vesztrocy , A W , Rodriguez , J M , Tress , M L , Frasca , M , Notaro , M , Grossi , G , Petrini , A , Re , M , Valentini , G , Mesiti , M , Roche , D B , Reeb , J , Ritchie , D W , Aridhi , S , Alborzi , S Z , Devignes , M-D , Koo , D C E , Bonneau , R , Gligorijevic , V , Barot , M , Fang , H , Toppo , S , Lavezzo , E , Falda , M , Berselli , M , Tosatto , S C E , Carraro , M , Piovesan , D , Rehman , H U , Mao , Q , Zhang , S , Vucetic , S , Black , G S , Jo , D , Suh , E , Dayton , J B , Larsen , D J , Omdahl , A R , McGuffin , L J , Brackenridge , D A , Babbitt , P C , Yunes , J M , Fontana , P , Zhang , F , Zhu , S , You , R , Zhang , Z , Dai , S , Yao , S , Tian , W , Cao , R , Chandler , C , Amezola , M , Johnson , D , Chang , J-M , Liao , W-H , Liu , Y-W , Pascarelli , S , Frank , Y , Hoehndorf , R , Kulmanov , M , Boudellioua , I , Politano , G , Di Carlo , S , Benso , A , Hakala , K , Ginter , F , Mehryary , F , Kaewphan , S , Bjorne , J , Moen , H , Tolvanen , M E E , Salakoski , T , Kihara , D , Jain , A , Smuc , T , Altenhoff , A , Ben-Hur , A , Rost , B , Brenner , S E , Orengo , C A , Jeffery , C J , Bosco , G , Hogan , D A , Martin , M J , O'Donovan , C , Mooney , S D , Greene , C S , Radivojac , P & Friedberg , I 2019 , ' The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens ' , Genome Biology , vol. 20 , no. 1 , 244 . https://doi.org/10.1186/s13059-019-1835-8Test; ORCID: /0000-0003-2482-0663/work/68617657; bbcc4816-628a-4e90-8797-a902971e0328; http://hdl.handle.net/10138/309448Test; 000498615000001
الإتاحة: http://hdl.handle.net/10138/309448Test
حقوق: cc_by ; openAccess ; info:eu-repo/semantics/openAccess
رقم الانضمام: edsbas.FCCA7563
قاعدة البيانات: BASE
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