RT Journal Article
SR Electronic
T1 The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 653105
DO 10.1101/653105
A1 Zhou, Naihui
A1 Jiang, Yuxiang
A1 Bergquist, Timothy R
A1 Lee, Alexandra J
A1 Kacsoh, Balint Z
A1 Crocker, Alex W
A1 Lewis, Kimberley A
A1 Georghiou, George
A1 Nguyen, Huy N
A1 Hamid, Md Nafiz
A1 Davis, Larry
A1 Dogan, Tunca
A1 Atalay, Volkan
A1 Rifaioglu, Ahmet S
A1 Dalkiran, Alperen
A1 Cetin-Atalay, Rengul
A1 Zhang, Chengxin
A1 Hurto, Rebecca L
A1 Freddolino, Peter L
A1 Zhang, Yang
A1 Bhat, Prajwal
A1 Supek, Fran
A1 Fernández, José M
A1 Gemovic, Branislava
A1 Perovic, Vladimir R
A1 Davidović, Radoslav S
A1 Sumonja, Neven
A1 Veljkovic, Nevena
A1 Asgari, Ehsaneddin
A1 Mofrad, Mohammad RK
A1 Profiti, Giuseppe
A1 Savojardo, Castrense
A1 Martelli, Pier Luigi
A1 Casadio, Rita
A1 Boecker, Florian
A1 Kahanda, Indika
A1 Thurlby, Natalie
A1 McHardy, Alice C
A1 Renaux, Alexandre
A1 Saidi, Rabie
A1 Gough, Julian
A1 Freitas, Alex A
A1 Antczak, Magdalena
A1 Fabris, Fabio
A1 Wass, Mark N
A1 Hou, Jie
A1 Cheng, Jianlin
A1 Hou, Jie
A1 Wang, Zheng
A1 Romero, Alfonso E
A1 Paccanaro, Alberto
A1 Yang, Haixuan
A1 Goldberg, Tatyana
A1 Zhao, Chenguang
A1 Holm, Liisa
A1 Törönen, Petri
A1 Medlar, Alan J
A1 Zosa, Elaine
A1 Borukhov, Itamar
A1 Novikov, Ilya
A1 Wilkins, Angela
A1 Lichtarge, Olivier
A1 Chi, Po-Han
A1 Tseng, Wei-Cheng
A1 Linial, Michal
A1 Rose, Peter W
A1 Dessimoz, Christophe
A1 Vidulin, Vedrana
A1 Dzeroski, Saso
A1 Sillitoe, Ian
A1 Das, Sayoni
A1 Lees, Jonathan Gill
A1 Jones, David T
A1 Wan, Cen
A1 Cozzetto, Domenico
A1 Fa, Rui
A1 Torres, Mateo
A1 Vesztrocy, Alex Wiarwick
A1 Rodriguez, Jose Manuel
A1 Tress, Michael L
A1 Frasca, Marco
A1 Notaro, Marco
A1 Grossi, Giuliano
A1 Petrini, Alessandro
A1 Re, Matteo
A1 Valentini, Giorgio
A1 Mesiti, Marco
A1 Roche, Daniel B
A1 Reeb, Jonas
A1 Ritchie, David W
A1 Aridhi, Sabeur
A1 Alborzi, Seyed Ziaeddin
A1 Devignes, Marie-Dominique
A1 Emily Koo, Da Chen
A1 Bonneau, Richard
A1 Gligorijević, Vladimir
A1 Barot, Meet
A1 Fang, Hai
A1 Toppo, Stefano
A1 Lavezzo, Enrico
A1 Falda, Marco
A1 Berselli, Michele
A1 Tosatto, Silvio CE
A1 Carraro, Marco
A1 Piovesan, Damiano
A1 Rehman, Hafeez Ur
A1 Mao, Qizhong
A1 Zhang, Shanshan
A1 Vucetic, Slobodan
A1 Black, Gage S
A1 Jo, Dane
A1 Larsen, Dallas J
A1 Omdahl, Ashton R
A1 Sagers, Luke W
A1 Suh, Erica
A1 Dayton, Jonathan B
A1 McGuffin, Liam J
A1 Brackenridge, Danielle A
A1 Babbitt, Patricia C
A1 Yunes, Jeffrey M
A1 Fontana, Paolo
A1 Zhang, Feng
A1 Zhu, Shanfeng
A1 You, Ronghui
A1 Zhang, Zihan
A1 Dai, Suyang
A1 Yao, Shuwei
A1 Tian, Weidong
A1 Cao, Renzhi
A1 Chandler, Caleb
A1 Amezola, Miguel
A1 Johnson, Devon
A1 Chang, Jia-Ming
A1 Liao, Wen-Hung
A1 Liu, Yi-Wei
A1 Pascarelli, Stefano
A1 Frank, Yotam
A1 Hoehndorf, Robert
A1 Kulmanov, Maxat
A1 Boudellioua, Imane
A1 Politano, Gianfranco
A1 Di Carlo, Stefano
A1 Benso, Alfredo
A1 Hakala, Kai
A1 Ginter, Filip
A1 Mehryary, Farrokh
A1 Kaewphan, Suwisa
A1 Björne, Jari
A1 Moen, Hans
A1 Tolvanen, Martti E E
A1 Salakoski, Tapio
A1 Kihara, Daisuke
A1 Jain, Aashish
A1 Šmuc, Tomislav
A1 Altenhoff, Adrian
A1 Ben-Hur, Asa
A1 Rost, Burkhard
A1 Brenner, Steven E
A1 Orengo, Christine A
A1 Jeffery, Constance J
A1 Bosco, Giovanni
A1 Hogan, Deborah A
A1 Martin, Maria J
A1 O’Donovan, Claire
A1 Mooney, Sean D
A1 Greene, Casey S
A1 Radivojac, Predrag
A1 Friedberg, Iddo
YR 2019
UL http://biorxiv.org/content/early/2019/05/29/653105.abstract
AB The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. 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 (P. aureginosa only). We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. 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 expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. We finally report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bioontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.