An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang; Tal Ronnen Oron; Wyatt T. Clark; Asma R. Bankapur; Daniel D'Andrea; Rosalba Lepore; Christopher S. Funk; Indika Kahanda; Karin M. Verspoor; Asa Ben-Hur; Da Chen Emily Koo; Duncan Penfold-Brown; Dennis Shasha; Noah Youngs; Richard Bonneau; Alexandra Lin; Sayed M.E. Sahraeian; Pier Luigi Martelli; Giuseppe Profiti; Rita Casadio; Renzhi Cao; Zhaolong Zhong; Jianlin Cheng; Adrian Altenhoff; Nives Skunca; Christophe Dessimoz; Tunca Dogan; Kai Hakala; Suwisa Kaewphan; Farrokh Mehryary; Tapio Salakoski; Filip Ginter; Hai Fang; Ben Smithers; Matt Oates; Julian Gough; Petri Törönen; Patrik Koskinen; Liisa Holm; Ching Tai Chen; Wen Lian Hsu; Kevin Bryson; Domenico Cozzetto; Federico Minneci; David T. Jones; Samuel Chapman; Dukka Bkc; Ishita K. Khan; Daisuke Kihara; Dan Ofer; Nadav Rappoport; Amos Stern; Elena Cibrian-Uhalte; Paul Denny; Rebecca E. Foulger; Reija Hieta; Duncan Legge; Ruth C. Lovering; Michele Magrane; Anna N. Melidoni; Prudence Mutowo-Meullenet; Klemens Pichler; Aleksandra Shypitsyna; Biao Li; Pooya Zakeri; Sarah ElShal; Léon Charles Tranchevent; Sayoni Das; Natalie L. Dawson; David Lee; Jonathan G. Lees; Ian Sillitoe; Prajwal Bhat; Tamás Nepusz; Alfonso E. Romero; Rajkumar Sasidharan; Haixuan Yang; Alberto Paccanaro; Jesse Gillis; Adriana E. Sedeño-Cortés; Paul Pavlidis; Shou Feng; Juan M. Cejuela; Tatyana Goldberg; Tobias Hamp; Lothar Richter; Asaf Salamov; Toni Gabaldon; Marina Marcet-Houben; Fran Supek; Qingtian Gong; Wei Ning; Yuanpeng Zhou; Weidong Tian; Marco Falda; Paolo Fontana; Enrico Lavezzo; Stefano Toppo; Carlo Ferrari; Manuel Giollo; Damiano Piovesan; Silvio C.E. Tosatto; Angela del Pozo; José M. Fernández; Paolo Maietta; Alfonso Valencia; Michael L. Tress; Alfredo Benso; Stefano Di Carlo; Gianfranco Politano; Alessandro Savino; Hafeez Ur Rehman; Matteo Re; Marco Mesiti; Giorgio Valentini; Joachim W. Bargsten; Aalt D.J. van Dijk; Branislava Gemovic; Sanja Glisic; Vladmir Perovic; Veljko Veljkovic; Nevena Veljkovic; Danillo C. Almeida-e-Silva; Ricardo Z.N. Vencio; Malvika Sharan; Jörg Vogel; Lakesh Kansakar; Shanshan Zhang; Slobodan Vucetic; Zheng Wang; Michael J.E. Sternberg; Mark N. Wass; Rachael P. Huntley; Maria J. Martin; Claire O'Donovan; Peter N. Robinson; Yves Moreau; Anna Tramontano; Patricia C. Babbitt; Steven E. Brenner; Michal Linial; Christine A. Orengo; Burkhard Rost; Casey S. Greene; Sean D. Mooney; Iddo Friedberg; Predrag Radivojac

doi:10.1186/s13059-016-1037-6

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang
, Tal Ronnen Oron
, Wyatt T. Clark
, Asma R. Bankapur
, Daniel D'Andrea
, Rosalba Lepore
, Christopher S. Funk
, Indika Kahanda
, Karin M. Verspoor
, Asa Ben-Hur
, Da Chen Emily Koo
, Duncan Penfold-Brown
, Dennis Shasha
, Noah Youngs
, Richard Bonneau
, Alexandra Lin
, Sayed M.E. Sahraeian
, Pier Luigi Martelli
, Giuseppe Profiti
, Rita Casadio

Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Skunca, Christophe Dessimoz, Tunca Dogan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching Tai Chen, Wen Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T. Jones, Samuel Chapman, Dukka Bkc, Ishita K. Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrian-Uhalte, Paul Denny, Rebecca E. Foulger, Reija Hieta, Duncan Legge, Ruth C. Lovering, Michele Magrane, Anna N. Melidoni, Prudence Mutowo-Meullenet, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon Charles Tranchevent, Sayoni Das, Natalie L. Dawson, David Lee, Jonathan G. Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E. Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E. Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan M. Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldon, Marina Marcet-Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo, Damiano Piovesan, Silvio C.E. Tosatto, Angela del Pozo, José M. Fernández, Paolo Maietta, Alfonso Valencia, Michael L. Tress, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Hafeez Ur Rehman, Matteo Re, Marco Mesiti, Giorgio Valentini, Joachim W. Bargsten, Aalt D.J. van Dijk, Branislava Gemovic, Sanja Glisic, Vladmir Perovic, Veljko Veljkovic, Nevena Veljkovic, Danillo C. Almeida-e-Silva, Ricardo Z.N. Vencio, Malvika Sharan, Jörg Vogel, Lakesh Kansakar, Shanshan Zhang, Slobodan Vucetic, Zheng Wang, Michael J.E. Sternberg, Mark N. Wass, Rachael P. Huntley, Maria J. Martin, Claire O'Donovan, Peter N. Robinson, Yves Moreau, Anna Tramontano, Patricia C. Babbitt, Steven E. Brenner, Michal Linial, Christine A. Orengo, Burkhard Rost, Casey S. Greene, Sean D. Mooney, Iddo Friedberg, Predrag Radivojac

Yale University
Miami University
Università di Roma la Sapienza
University of Colorado School of Medicine
University of Melbourne
University of California, Berkeley
Dipartimento di Astronomia, Università di Bologna
ETH Zurich
University College London
University of Turku
Université Claude Bernard Lyon 1
University of California, Los Angeles
National University of Ireland Galway
The University of British Columbia
Physik-department, Technische Universität München
Institució Catalana de Recerca i Estudis Avan ats (ICREA)
University of Osijek
University of Padova
Fondazione Edmund Mach
Instituto de Astronomia, Geofísica e Cincias Atmosféricas, Universidade de São Paulo
Institut für Theoretische Physik and Astrophysik, Universität Würzburg
University of Southern Mississippi
Imperial College London
University of California San Francisco
University of Pennsylvania

Producción científica: Article › revisión exhaustiva

Idioma original	English
Número de artículo	184
Publicación	Genome Biology
Volumen	17
N.º	1
DOI	https://doi.org/10.1186/s13059-016-1037-6
Estado	Published - sept 7 2016
Publicado de forma externa	Sí

ASJC Scopus Subject Areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Acceder al documento

10.1186/s13059-016-1037-6

Otros archivos y enlaces

Citar esto

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., ... Radivojac, P. (2016). An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, 17(1), Artículo 184. https://doi.org/10.1186/s13059-016-1037-6

Jiang, Y, Oron, TR, Clark, WT, Bankapur, AR, D'Andrea, D, Lepore, R, Funk, CS, Kahanda, I, Verspoor, KM, Ben-Hur, A, Koo, DCE, Penfold-Brown, D, Shasha, D, Youngs, N, Bonneau, R, Lin, A, Sahraeian, SME, Martelli, PL, Profiti, G, Casadio, R, Cao, R, Zhong, Z, Cheng, J, Altenhoff, A, Skunca, N, Dessimoz, C, Dogan, T, Hakala, K, Kaewphan, S, Mehryary, F, Salakoski, T, Ginter, F, Fang, H, Smithers, B, Oates, M, Gough, J, Törönen, P, Koskinen, P, Holm, L, Chen, CT, Hsu, WL, Bryson, K, Cozzetto, D, Minneci, F, Jones, DT, Chapman, S, Bkc, D, Khan, IK, Kihara, D, Ofer, D, Rappoport, N, Stern, A, Cibrian-Uhalte, E, Denny, P, Foulger, RE, Hieta, R, Legge, D, Lovering, RC, Magrane, M, Melidoni, AN, Mutowo-Meullenet, P, Pichler, K, Shypitsyna, A, Li, B, Zakeri, P, ElShal, S, Tranchevent, LC, Das, S, Dawson, NL, Lee, D, Lees, JG, Sillitoe, I, Bhat, P, Nepusz, T, Romero, AE, Sasidharan, R, Yang, H, Paccanaro, A, Gillis, J, Sedeño-Cortés, AE, Pavlidis, P, Feng, S, Cejuela, JM, Goldberg, T, Hamp, T, Richter, L, Salamov, A, Gabaldon, T, Marcet-Houben, M, Supek, F, Gong, Q, Ning, W, Zhou, Y, Tian, W, Falda, M, Fontana, P, Lavezzo, E, Toppo, S, Ferrari, C, Giollo, M, Piovesan, D, Tosatto, SCE, del Pozo, A, Fernández, JM, Maietta, P, Valencia, A, Tress, ML, Benso, A, Di Carlo, S, Politano, G, Savino, A, Rehman, HU, Re, M, Mesiti, M, Valentini, G, Bargsten, JW, van Dijk, ADJ, Gemovic, B, Glisic, S, Perovic, V, Veljkovic, V, Veljkovic, N, Almeida-e-Silva, DC, Vencio, RZN, Sharan, M, Vogel, J, Kansakar, L, Zhang, S, Vucetic, S, Wang, Z, Sternberg, MJE, Wass, MN, Huntley, RP, Martin, MJ, O'Donovan, C, Robinson, PN, Moreau, Y, Tramontano, A, Babbitt, PC, Brenner, SE, Linial, M, Orengo, CA, Rost, B, Greene, CS, Mooney, SD, Friedberg, I & Radivojac, P 2016, 'An expanded evaluation of protein function prediction methods shows an improvement in accuracy', Genome Biology, vol. 17, n.º 1, 184. https://doi.org/10.1186/s13059-016-1037-6

@article{9835c1c35cb44a10a8d710b4c7bfecef,

title = "An expanded evaluation of protein function prediction methods shows an improvement in accuracy",

keywords = "Disease gene prioritization, Protein function prediction",

author = "Yuxiang Jiang and Oron, \{Tal Ronnen\} and Clark, \{Wyatt T.\} and Bankapur, \{Asma R.\} and Daniel D'Andrea and Rosalba Lepore and Funk, \{Christopher S.\} and Indika Kahanda and Verspoor, \{Karin M.\} and Asa Ben-Hur and Koo, \{Da Chen Emily\} and Duncan Penfold-Brown and Dennis Shasha and Noah Youngs and Richard Bonneau and Alexandra Lin and Sahraeian, \{Sayed M.E.\} and Martelli, \{Pier Luigi\} and Giuseppe Profiti and Rita Casadio and Renzhi Cao and Zhaolong Zhong and Jianlin Cheng and Adrian Altenhoff and Nives Skunca and Christophe Dessimoz and Tunca Dogan and Kai Hakala and Suwisa Kaewphan and Farrokh Mehryary and Tapio Salakoski and Filip Ginter and Hai Fang and Ben Smithers and Matt Oates and Julian Gough and Petri T{\"o}r{\"o}nen and Patrik Koskinen and Liisa Holm and Chen, \{Ching Tai\} and Hsu, \{Wen Lian\} and Kevin Bryson and Domenico Cozzetto and Federico Minneci and Jones, \{David T.\} and Samuel Chapman and Dukka Bkc and Khan, \{Ishita K.\} and Daisuke Kihara and Dan Ofer and Nadav Rappoport and Amos Stern and Elena Cibrian-Uhalte and Paul Denny and Foulger, \{Rebecca E.\} and Reija Hieta and Duncan Legge and Lovering, \{Ruth C.\} and Michele Magrane and Melidoni, \{Anna N.\} and Prudence Mutowo-Meullenet and Klemens Pichler and Aleksandra Shypitsyna and Biao Li and Pooya Zakeri and Sarah ElShal and Tranchevent, \{L{\'e}on Charles\} and Sayoni Das and Dawson, \{Natalie L.\} and David Lee and Lees, \{Jonathan G.\} and Ian Sillitoe and Prajwal Bhat and Tam{\'a}s Nepusz and Romero, \{Alfonso E.\} and Rajkumar Sasidharan and Haixuan Yang and Alberto Paccanaro and Jesse Gillis and Sede{\~n}o-Cort{\'e}s, \{Adriana E.\} and Paul Pavlidis and Shou Feng and Cejuela, \{Juan M.\} and Tatyana Goldberg and Tobias Hamp and Lothar Richter and Asaf Salamov and Toni Gabaldon and Marina Marcet-Houben and Fran Supek and Qingtian Gong and Wei Ning and Yuanpeng Zhou and Weidong Tian and Marco Falda and Paolo Fontana and Enrico Lavezzo and Stefano Toppo and Carlo Ferrari and Manuel Giollo and Damiano Piovesan and Tosatto, \{Silvio C.E.\} and \{del Pozo\}, Angela and Fern{\'a}ndez, \{Jos{\'e} M.\} and Paolo Maietta and Alfonso Valencia and Tress, \{Michael L.\} and Alfredo Benso and \{Di Carlo\}, Stefano and Gianfranco Politano and Alessandro Savino and Rehman, \{Hafeez Ur\} and Matteo Re and Marco Mesiti and Giorgio Valentini and Bargsten, \{Joachim W.\} and \{van Dijk\}, \{Aalt D.J.\} and Branislava Gemovic and Sanja Glisic and Vladmir Perovic and Veljko Veljkovic and Nevena Veljkovic and Almeida-e-Silva, \{Danillo C.\} and Vencio, \{Ricardo Z.N.\} and Malvika Sharan and J{\"o}rg Vogel and Lakesh Kansakar and Shanshan Zhang and Slobodan Vucetic and Zheng Wang and Sternberg, \{Michael J.E.\} and Wass, \{Mark N.\} and Huntley, \{Rachael P.\} and Martin, \{Maria J.\} and Claire O'Donovan and Robinson, \{Peter N.\} and Yves Moreau and Anna Tramontano and Babbitt, \{Patricia C.\} and Brenner, \{Steven E.\} and Michal Linial and Orengo, \{Christine A.\} and Burkhard Rost and Greene, \{Casey S.\} and Mooney, \{Sean D.\} and Iddo Friedberg and Predrag Radivojac",

note = "Publisher Copyright: {\textcopyright} 2016 The Author(s).",

year = "2016",

month = sep,

day = "7",

doi = "10.1186/s13059-016-1037-6",

language = "English",

volume = "17",

number = "1",

}

TY - JOUR

T1 - An expanded evaluation of protein function prediction methods shows an improvement in accuracy

AU - Jiang, Yuxiang

AU - Oron, Tal Ronnen

AU - Clark, Wyatt T.

AU - Bankapur, Asma R.

AU - D'Andrea, Daniel

AU - Lepore, Rosalba

AU - Funk, Christopher S.

AU - Kahanda, Indika

AU - Verspoor, Karin M.

AU - Ben-Hur, Asa

AU - Koo, Da Chen Emily

AU - Penfold-Brown, Duncan

AU - Shasha, Dennis

AU - Youngs, Noah

AU - Bonneau, Richard

AU - Lin, Alexandra

AU - Sahraeian, Sayed M.E.

AU - Martelli, Pier Luigi

AU - Profiti, Giuseppe

AU - Casadio, Rita

AU - Cao, Renzhi

AU - Zhong, Zhaolong

AU - Cheng, Jianlin

AU - Altenhoff, Adrian

AU - Skunca, Nives

AU - Dessimoz, Christophe

AU - Dogan, Tunca

AU - Hakala, Kai

AU - Kaewphan, Suwisa

AU - Mehryary, Farrokh

AU - Salakoski, Tapio

AU - Ginter, Filip

AU - Fang, Hai

AU - Smithers, Ben

AU - Oates, Matt

AU - Gough, Julian

AU - Törönen, Petri

AU - Koskinen, Patrik

AU - Holm, Liisa

AU - Chen, Ching Tai

AU - Hsu, Wen Lian

AU - Bryson, Kevin

AU - Cozzetto, Domenico

AU - Minneci, Federico

AU - Jones, David T.

AU - Chapman, Samuel

AU - Bkc, Dukka

AU - Khan, Ishita K.

AU - Kihara, Daisuke

AU - Ofer, Dan

AU - Rappoport, Nadav

AU - Stern, Amos

AU - Cibrian-Uhalte, Elena

AU - Denny, Paul

AU - Foulger, Rebecca E.

AU - Hieta, Reija

AU - Legge, Duncan

AU - Lovering, Ruth C.

AU - Magrane, Michele

AU - Melidoni, Anna N.

AU - Mutowo-Meullenet, Prudence

AU - Pichler, Klemens

AU - Shypitsyna, Aleksandra

AU - Li, Biao

AU - Zakeri, Pooya

AU - ElShal, Sarah

AU - Tranchevent, Léon Charles

AU - Das, Sayoni

AU - Dawson, Natalie L.

AU - Lee, David

AU - Lees, Jonathan G.

AU - Sillitoe, Ian

AU - Bhat, Prajwal

AU - Nepusz, Tamás

AU - Romero, Alfonso E.

AU - Sasidharan, Rajkumar

AU - Yang, Haixuan

AU - Paccanaro, Alberto

AU - Gillis, Jesse

AU - Sedeño-Cortés, Adriana E.

AU - Pavlidis, Paul

AU - Feng, Shou

AU - Cejuela, Juan M.

AU - Goldberg, Tatyana

AU - Hamp, Tobias

AU - Richter, Lothar

AU - Salamov, Asaf

AU - Gabaldon, Toni

AU - Marcet-Houben, Marina

AU - Supek, Fran

AU - Gong, Qingtian

AU - Ning, Wei

AU - Zhou, Yuanpeng

AU - Tian, Weidong

AU - Falda, Marco

AU - Fontana, Paolo

AU - Lavezzo, Enrico

AU - Toppo, Stefano

AU - Ferrari, Carlo

AU - Giollo, Manuel

AU - Piovesan, Damiano

AU - Tosatto, Silvio C.E.

AU - del Pozo, Angela

AU - Fernández, José M.

AU - Maietta, Paolo

AU - Valencia, Alfonso

AU - Tress, Michael L.

AU - Benso, Alfredo

AU - Di Carlo, Stefano

AU - Politano, Gianfranco

AU - Savino, Alessandro

AU - Rehman, Hafeez Ur

AU - Re, Matteo

AU - Mesiti, Marco

AU - Valentini, Giorgio

AU - Bargsten, Joachim W.

AU - van Dijk, Aalt D.J.

AU - Gemovic, Branislava

AU - Glisic, Sanja

AU - Perovic, Vladmir

AU - Veljkovic, Veljko

AU - Veljkovic, Nevena

AU - Almeida-e-Silva, Danillo C.

AU - Vencio, Ricardo Z.N.

AU - Sharan, Malvika

AU - Vogel, Jörg

AU - Kansakar, Lakesh

AU - Zhang, Shanshan

AU - Vucetic, Slobodan

AU - Wang, Zheng

AU - Sternberg, Michael J.E.

AU - Wass, Mark N.

AU - Huntley, Rachael P.

AU - Martin, Maria J.

AU - O'Donovan, Claire

AU - Robinson, Peter N.

AU - Moreau, Yves

AU - Tramontano, Anna

AU - Babbitt, Patricia C.

AU - Brenner, Steven E.

AU - Linial, Michal

AU - Orengo, Christine A.

AU - Rost, Burkhard

AU - Greene, Casey S.

AU - Mooney, Sean D.

AU - Friedberg, Iddo

AU - Radivojac, Predrag

PY - 2016/9/7

Y1 - 2016/9/7

KW - Disease gene prioritization

KW - Protein function prediction

UR - https://www.scopus.com/pages/publications/84986207718

UR - https://www.scopus.com/pages/publications/84986207718#tab=citedBy

U2 - 10.1186/s13059-016-1037-6

DO - 10.1186/s13059-016-1037-6

M3 - Article

C2 - 27604469

AN - SCOPUS:84986207718

SN - 1474-7596

VL - 17

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 184

ER -

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

ASJC Scopus Subject Areas

Acceder al documento

Otros archivos y enlaces

Huella

Citar esto