Abstract
Original language | English (US) |
---|---|
Journal | Genome biology |
Volume | 20 |
Issue number | 1 |
DOIs | |
State | Published - Nov 19 2019 |
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. / 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; Dalkıran, Alperen; Cetin Atalay, Rengul; Zhang, Chengxin; Hurto, Rebecca L; Freddolino, Peter L; Zhang, Yang; Bhat, Prajwal; Supek, Fran; Fernández, José M; Gemovic, Branislava; Perovic, Vladimir R; Davidović, 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; Warwick Vesztrocy, Alex; 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; Gligorijević, Vladimir; Barot, Meet; Fang, Hai; Toppo, Stefano; Lavezzo, Enrico; Falda, Marco; Berselli, Michele; Tosatto, Silvio C E; Carraro, Marco; Piovesan, Damiano; Ur Rehman, Hafeez; 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, Imene; Politano, Gianfranco; Di Carlo, Stefano; Benso, Alfredo; Hakala, Kai; Ginter, Filip; Mehryary, Farrokh; Kaewphan, Suwisa; Björne, Jari; Moen, Hans; Tolvanen, Martti E E; Salakoski, Tapio; Kihara, Daisuke; Jain, Aashish; Šmuc, 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.
In: Genome biology, Vol. 20, No. 1, 19.11.2019.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
AU - Zhou, Naihui
AU - Jiang, Yuxiang
AU - Bergquist, Timothy R
AU - Lee, Alexandra J
AU - Kacsoh, Balint Z
AU - Crocker, Alex W
AU - Lewis, Kimberley A
AU - Georghiou, George
AU - Nguyen, Huy N
AU - Hamid, Md Nafiz
AU - Davis, Larry
AU - Dogan, Tunca
AU - Atalay, Volkan
AU - Rifaioglu, Ahmet S
AU - Dalkıran, Alperen
AU - Cetin Atalay, Rengul
AU - Zhang, Chengxin
AU - Hurto, Rebecca L
AU - Freddolino, Peter L
AU - Zhang, Yang
AU - Bhat, Prajwal
AU - Supek, Fran
AU - Fernández, José M
AU - Gemovic, Branislava
AU - Perovic, Vladimir R
AU - Davidović, Radoslav S
AU - Sumonja, Neven
AU - Veljkovic, Nevena
AU - Asgari, Ehsaneddin
AU - Mofrad, Mohammad R K
AU - Profiti, Giuseppe
AU - Savojardo, Castrense
AU - Martelli, Pier Luigi
AU - Casadio, Rita
AU - Boecker, Florian
AU - Schoof, Heiko
AU - Kahanda, Indika
AU - Thurlby, Natalie
AU - McHardy, Alice C
AU - Renaux, Alexandre
AU - Saidi, Rabie
AU - Gough, Julian
AU - Freitas, Alex A
AU - Antczak, Magdalena
AU - Fabris, Fabio
AU - Wass, Mark N
AU - Hou, Jie
AU - Cheng, Jianlin
AU - Wang, Zheng
AU - Romero, Alfonso E
AU - Paccanaro, Alberto
AU - Yang, Haixuan
AU - Goldberg, Tatyana
AU - Zhao, Chenguang
AU - Holm, Liisa
AU - Törönen, Petri
AU - Medlar, Alan J
AU - Zosa, Elaine
AU - Borukhov, Itamar
AU - Novikov, Ilya
AU - Wilkins, Angela
AU - Lichtarge, Olivier
AU - Chi, Po-Han
AU - Tseng, Wei-Cheng
AU - Linial, Michal
AU - Rose, Peter W
AU - Dessimoz, Christophe
AU - Vidulin, Vedrana
AU - Dzeroski, Saso
AU - Sillitoe, Ian
AU - Das, Sayoni
AU - Lees, Jonathan Gill
AU - Jones, David T
AU - Wan, Cen
AU - Cozzetto, Domenico
AU - Fa, Rui
AU - Torres, Mateo
AU - Warwick Vesztrocy, Alex
AU - Rodriguez, Jose Manuel
AU - Tress, Michael L
AU - Frasca, Marco
AU - Notaro, Marco
AU - Grossi, Giuliano
AU - Petrini, Alessandro
AU - Re, Matteo
AU - Valentini, Giorgio
AU - Mesiti, Marco
AU - Roche, Daniel B
AU - Reeb, Jonas
AU - Ritchie, David W
AU - Aridhi, Sabeur
AU - Alborzi, Seyed Ziaeddin
AU - Devignes, Marie-Dominique
AU - Koo, Da Chen Emily
AU - Bonneau, Richard
AU - Gligorijević, Vladimir
AU - Barot, Meet
AU - Fang, Hai
AU - Toppo, Stefano
AU - Lavezzo, Enrico
AU - Falda, Marco
AU - Berselli, Michele
AU - Tosatto, Silvio C E
AU - Carraro, Marco
AU - Piovesan, Damiano
AU - Ur Rehman, Hafeez
AU - Mao, Qizhong
AU - Zhang, Shanshan
AU - Vucetic, Slobodan
AU - Black, Gage S
AU - Jo, Dane
AU - Suh, Erica
AU - Dayton, Jonathan B
AU - Larsen, Dallas J
AU - Omdahl, Ashton R
AU - McGuffin, Liam J
AU - Brackenridge, Danielle A
AU - Babbitt, Patricia C
AU - Yunes, Jeffrey M
AU - Fontana, Paolo
AU - Zhang, Feng
AU - Zhu, Shanfeng
AU - You, Ronghui
AU - Zhang, Zihan
AU - Dai, Suyang
AU - Yao, Shuwei
AU - Tian, Weidong
AU - Cao, Renzhi
AU - Chandler, Caleb
AU - Amezola, Miguel
AU - Johnson, Devon
AU - Chang, Jia-Ming
AU - Liao, Wen-Hung
AU - Liu, Yi-Wei
AU - Pascarelli, Stefano
AU - Frank, Yotam
AU - Hoehndorf, Robert
AU - Kulmanov, Maxat
AU - Boudellioua, Imene
AU - Politano, Gianfranco
AU - Di Carlo, Stefano
AU - Benso, Alfredo
AU - Hakala, Kai
AU - Ginter, Filip
AU - Mehryary, Farrokh
AU - Kaewphan, Suwisa
AU - Björne, Jari
AU - Moen, Hans
AU - Tolvanen, Martti E E
AU - Salakoski, Tapio
AU - Kihara, Daisuke
AU - Jain, Aashish
AU - Šmuc, Tomislav
AU - Altenhoff, Adrian
AU - Ben-Hur, Asa
AU - Rost, Burkhard
AU - Brenner, Steven E
AU - Orengo, Christine A
AU - Jeffery, Constance J
AU - Bosco, Giovanni
AU - Hogan, Deborah A
AU - Martin, Maria J
AU - O'Donovan, Claire
AU - Mooney, Sean D
AU - Greene, Casey S
AU - Radivojac, Predrag
AU - Friedberg, Iddo
N1 - KAUST Repository Item: Exported on 2020-04-23 Acknowledged KAUST grant number(s): URF/1/3454-01-01 and URF/1/3790-01-01 Acknowledgements: NZ and IF acknowledge the invaluable input from Michael C Gerten and Shatabdi Sen and all members of the Friedberg Lab for the ongoing support for stimulating discussions.
PY - 2019/11/19
Y1 - 2019/11/19
N2 - 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.
AB - 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.
UR - http://hdl.handle.net/10754/660434
UR - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1835-8
UR - http://www.scopus.com/inward/record.url?scp=85075272104&partnerID=8YFLogxK
U2 - 10.1186/s13059-019-1835-8
DO - 10.1186/s13059-019-1835-8
M3 - Article
C2 - 31744546
VL - 20
JO - Genome Biology
JF - Genome Biology
SN - 1465-6914
IS - 1
ER -