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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
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...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930/ https://www.ncbi.nlm.nih.gov/pubmed/31744546 http://dx.doi.org/10.1186/s13059-019-1835-8 |
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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. 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, Imane 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 |
author_facet | 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, Imane 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 |
author_sort | Zhou, Naihui |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6864930 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-68649302019-11-29 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, Imane 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 Genome Biol Research 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. BioMed Central 2019-11-19 /pmc/articles/PMC6864930/ /pubmed/31744546 http://dx.doi.org/10.1186/s13059-019-1835-8 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research 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, Imane 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 The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens |
title | The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens |
title_full | The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens |
title_fullStr | The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens |
title_full_unstemmed | The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens |
title_short | The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens |
title_sort | cafa challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930/ https://www.ncbi.nlm.nih.gov/pubmed/31744546 http://dx.doi.org/10.1186/s13059-019-1835-8 |
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