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

Naihui Zhou; Yuxiang Jiang; Timothy R. Bergquist; Alexandra J. Lee; Balint Z. Kacsoh; Alex W. Crocker; Kimberley A. Lewis; George Georghiou; Huy N. Nguyen; Md Nafiz Hamid; Larry Davis; Tunca Dogan; Volkan Atalay; Ahmet S. Rifaioglu; Alperen Dalkıran; Rengul Cetin Atalay; Chengxin Zhang; Rebecca L. Hurto; Peter L. Freddolino; Yang Zhang; Prajwal Bhat; Fran Supek; José M. Fernández; Branislava Gemovic; Vladimir R. Perovic; Radoslav S. Davidović; Neven Sumonja; Nevena Veljkovic; Ehsaneddin Asgari; Mohammad R.K. Mofrad; Giuseppe Profiti; Castrense Savojardo; Pier Luigi Martelli; Rita Casadio; Florian Boecker; Heiko Schoof; Indika Kahanda; Natalie Thurlby; Alice C. McHardy; Alexandre Renaux; Rabie Saidi; Julian Gough; Alex A. Freitas; Magdalena Antczak; Fabio Fabris; Mark N. Wass; Jie Hou; Jianlin Cheng; Zheng Wang; Alfonso E. Romero; Alberto Paccanaro; Haixuan Yang; Tatyana Goldberg; Chenguang Zhao; Liisa Holm; Petri Törönen; Alan J. Medlar; Elaine Zosa; Itamar Borukhov; Ilya Novikov; Angela Wilkins; Olivier Lichtarge; Po-Han Chi; Wei-Cheng Tseng; Michal Linial; Peter W. Rose; Christophe Dessimoz; Vedrana Vidulin; Saso Dzeroski; Ian Sillitoe; Sayoni Das; Jonathan Gill Lees; David T. Jones; Cen Wan; Domenico Cozzetto; Rui Fa; Mateo Torres; Alex Warwick Vesztrocy; Jose Manuel Rodriguez; Michael L. Tress; Marco Frasca; Marco Notaro; Giuliano Grossi; Alessandro Petrini; Matteo Re; Giorgio Valentini; Marco Mesiti; Daniel B. Roche; Jonas Reeb; David W. Ritchie; Sabeur Aridhi; Seyed Ziaeddin Alborzi; Marie-Dominique Devignes; Da Chen Emily Koo; Richard Bonneau; Vladimir Gligorijević; Meet Barot; Hai Fang; Stefano Toppo; Enrico Lavezzo; Marco Falda; Michele Berselli; Silvio C.E. Tosatto; Marco Carraro; Damiano Piovesan; Hafeez Ur Rehman; Qizhong Mao; Shanshan Zhang; Slobodan Vucetic; Gage S. Black; Dane Jo; Erica Suh; Jonathan B. Dayton; Dallas J. Larsen; Ashton R. Omdahl; Liam J. McGuffin; Danielle A. Brackenridge; Patricia C. Babbitt; Jeffrey M. Yunes; Paolo Fontana; Feng Zhang; Shanfeng Zhu; Ronghui You; Zihan Zhang; Suyang Dai; Shuwei Yao; Weidong Tian; Renzhi Cao; Caleb Chandler; Miguel Amezola; Devon Johnson; Jia-Ming Chang; Wen-Hung Liao; Yi-Wei Liu; Stefano Pascarelli; Yotam Frank; Robert Hoehndorf; Maxat Kulmanov; Imane Boudellioua; Gianfranco Politano; Stefano Di Carlo; Alfredo Benso; Kai Hakala; Filip Ginter; Farrokh Mehryary; Suwisa Kaewphan; Jari Björne; Hans Moen; Martti E.E. Tolvanen; Tapio Salakoski; Daisuke Kihara; Aashish Jain; Tomislav Šmuc; Adrian Altenhoff; Asa Ben-Hur; Burkhard Rost; Steven E. Brenner; Christine A. Orengo; Constance J. Jeffery; Giovanni Bosco; Deborah A. Hogan; Maria J. Martin; Claire O’Donovan; Sean D. Mooney; Casey S. Greene; Predrag Radivojac; Iddo Friedberg

doi:10.1186/s13059-019-1835-8

Table 3 Baseline methods in term-centric evaluation of protein function prediction

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

	Model number	Training data	Score assignment
Expression	1	Gene expression compendium for P. aeruginosa PAO1	Highest correlation score out of all pairwise correlations
	2		Top 10 average correlation score
BLAST	1	All experimental annotation in UniProt-GOA. Sequences from Swiss-Prot	Highest sequence identity out of all pairwise BLASTp hits
	2	All experimental annotation in UniProt-GOA. Sequences from Swiss-Prot and TrEMBL
blastcomp	1	All experimental and computational annotations in UniProt-GOA. Sequences from Swiss-Prot
	2	All experimental and computational annotations in UniProt-GOA. Sequences from Swiss-Prot and TrEMBL

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