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

Show full item record



Permalink

http://hdl.handle.net/10138/309448

Citation

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/s13059-019-1835-8

Title: The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Author: 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
Contributor: University of Helsinki, Computational genomics
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Discovery Research Group/Prof. Hannu Toivonen
Date: 2019-11-19
Language: eng
Number of pages: 23
Belongs to series: Genome Biology
ISSN: 1474-760X
URI: http://hdl.handle.net/10138/309448
Abstract: 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.
Subject: Protein function prediction
Long-term memory
Biofilm
Critical assessment
Community challenge
CANDIDA-ALBICANS
ONTOLOGY
IDENTIFICATION
GENERATION
LIBRARY
318 Medical biotechnology
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
document.pdf 8.142Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record