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Pregled bibliografske jedinice broj: 1252143

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 et al.
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens // Genome Biology, 20 (2019), 1; 244, 23 doi:10.1186/s13059-019-1835-8 (međunarodna recenzija, članak, znanstveni)

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

Autori
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

Izvornik
Genome Biology (1474-760X) 20 (2019), 1; 244, 23

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
protein function prediction

Sažetak
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.

Izvorni jezik
Engleski



POVEZANOST RADA

Profili:

Avatar Url Fran Supek (autor)

Avatar Url Tomislav Šmuc (autor)

Avatar Url Vedrana Vidulin (autor)

Poveznice na cjeloviti tekst rada:

doi genomebiology.biomedcentral.com

Citiraj ovu publikaciju:

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 et al.
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens // Genome Biology, 20 (2019), 1; 244, 23 doi:10.1186/s13059-019-1835-8 (međunarodna recenzija, članak, znanstveni)
Zhou, N., Jiang, Y., Bergquist, T., Lee, A., Kacsoh, B., Crocker, A., Lewis, K., Georghiou, G., Nguyen, H. & Hamid, M. (2019) The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20 (1), 244, 23 doi:10.1186/s13059-019-1835-8.
@article{article, author = {Zhou, Naihui and Jiang, Yuxiang and Bergquist, Timothy R. and Lee, Alexandra J. and Kacsoh, Balint Z. and Crocker, Alex W. and Lewis, Kimberley A. and Georghiou, George and Nguyen, Huy N. and Hamid, Md Nafiz and Davis, Larry and Dogan, Tunca and Atalay, Volkan and Rifaioglu, Ahmet S. and Dalk\iran, Alperen and Cetin Atalay, Rengul and Zhang, Chengxin and Hurto, Rebecca L. and Freddolino, Peter L. and Zhang, Yang and Bhat, Prajwal and Supek, Fran and Fern\'{a}ndez, Jos\'{e} M. and Gemovic, Branislava and Perovic, Vladimir R. and Davidovi\'{c}, Radoslav S. and Sumonja, Neven and Veljkovic, Nevena and Asgari, Ehsaneddin and Mofrad, Mohammad R.K. and Profiti, Giuseppe and Savojardo, Castrense and Martelli, Pier Luigi and Casadio, Rita and Boecker, Florian and Schoof, Heiko and Kahanda, Indika and Thurlby, Natalie and McHardy, Alice C. and Renaux, Alexandre and Saidi, Rabie and Gough, Julian and Freitas, Alex A. and Antczak, Magdalena and Fabris, Fabio and Wass, Mark N. and Hou, Jie and Cheng, Jianlin and Wang, Zheng and Romero, Alfonso E. and Paccanaro, Alberto and Yang, Haixuan and Goldberg, Tatyana and Zhao, Chenguang and Holm, Liisa and T\"{o}r\"{o}nen, Petri and Medlar, Alan J. and Zosa, Elaine and Borukhov, Itamar and Novikov, Ilya and Wilkins, Angela and Lichtarge, Olivier and Chi, Po-Han and Tseng, Wei-Cheng and Linial, Michal and Rose, Peter W. and Dessimoz, Christophe and Vidulin, Vedrana and Dzeroski, Saso and Sillitoe, Ian and Das, Sayoni and Lees, Jonathan Gill and Jones, David T. and Wan, Cen and Cozzetto, Domenico and Fa, Rui and Torres, Mateo and Warwick Vesztrocy, Alex and Rodriguez, Jose Manuel and Tress, Michael L. and Frasca, Marco and Notaro, Marco and Grossi, Giuliano and Petrini, Alessandro and Re, Matteo and Valentini, Giorgio and Mesiti, Marco and Roche, Daniel B. and Reeb, Jonas and Ritchie, David W. and Aridhi, Sabeur and Alborzi, Seyed Ziaeddin and Devignes, Marie-Dominique and Koo, Da Chen Emily and Bonneau, Richard and Gligorijevi\'{c}, Vladimir and Barot, Meet and Fang, Hai and Toppo, Stefano and Lavezzo, Enrico and Falda, Marco and Berselli, Michele and Tosatto, Silvio C.E. and Carraro, Marco and Piovesan, Damiano and Ur Rehman, Hafeez and Mao, Qizhong and Zhang, Shanshan and Vucetic, Slobodan and Black, Gage S. and Jo, Dane and Suh, Erica and Dayton, Jonathan B. and Larsen, Dallas J. and Omdahl, Ashton R. and McGuffin, Liam J. and Brackenridge, Danielle A. and Babbitt, Patricia C. and Yunes, Jeffrey M. and Fontana, Paolo and Zhang, Feng and Zhu, Shanfeng and You, Ronghui and Zhang, Zihan and Dai, Suyang and Yao, Shuwei and Tian, Weidong and Cao, Renzhi and Chandler, Caleb and Amezola, Miguel and Johnson, Devon and Chang, Jia-Ming and Liao, Wen-Hung and Liu, Yi-Wei and Pascarelli, Stefano and Frank, Yotam and Hoehndorf, Robert and Kulmanov, Maxat and Boudellioua, Imane and Politano, Gianfranco and Di Carlo, Stefano and Benso, Alfredo and Hakala, Kai and Ginter, Filip and Mehryary, Farrokh and Kaewphan, Suwisa and Bj\"{o}rne, Jari and Moen, Hans and Tolvanen, Martti E.E. and Salakoski, Tapio and Kihara, Daisuke and Jain, Aashish and \v{S}muc, Tomislav and Altenhoff, Adrian and Ben-Hur, Asa and Rost, Burkhard and Brenner, Steven E. and Orengo, Christine A. and Jeffery, Constance J. and Bosco, Giovanni and Hogan, Deborah A. and Martin, Maria J. and O’Donovan, Claire and Mooney, Sean D. and Greene, Casey S. and Radivojac, Predrag and Friedberg, Iddo}, year = {2019}, pages = {23}, DOI = {10.1186/s13059-019-1835-8}, chapter = {244}, keywords = {protein function prediction}, journal = {Genome Biology}, doi = {10.1186/s13059-019-1835-8}, volume = {20}, number = {1}, issn = {1474-760X}, title = {The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens}, keyword = {protein function prediction}, chapternumber = {244} }
@article{article, author = {Zhou, Naihui and Jiang, Yuxiang and Bergquist, Timothy R. and Lee, Alexandra J. and Kacsoh, Balint Z. and Crocker, Alex W. and Lewis, Kimberley A. and Georghiou, George and Nguyen, Huy N. and Hamid, Md Nafiz and Davis, Larry and Dogan, Tunca and Atalay, Volkan and Rifaioglu, Ahmet S. and Dalk\iran, Alperen and Cetin Atalay, Rengul and Zhang, Chengxin and Hurto, Rebecca L. and Freddolino, Peter L. and Zhang, Yang and Bhat, Prajwal and Supek, Fran and Fern\'{a}ndez, Jos\'{e} M. and Gemovic, Branislava and Perovic, Vladimir R. and Davidovi\'{c}, Radoslav S. and Sumonja, Neven and Veljkovic, Nevena and Asgari, Ehsaneddin and Mofrad, Mohammad R.K. and Profiti, Giuseppe and Savojardo, Castrense and Martelli, Pier Luigi and Casadio, Rita and Boecker, Florian and Schoof, Heiko and Kahanda, Indika and Thurlby, Natalie and McHardy, Alice C. and Renaux, Alexandre and Saidi, Rabie and Gough, Julian and Freitas, Alex A. and Antczak, Magdalena and Fabris, Fabio and Wass, Mark N. and Hou, Jie and Cheng, Jianlin and Wang, Zheng and Romero, Alfonso E. and Paccanaro, Alberto and Yang, Haixuan and Goldberg, Tatyana and Zhao, Chenguang and Holm, Liisa and T\"{o}r\"{o}nen, Petri and Medlar, Alan J. and Zosa, Elaine and Borukhov, Itamar and Novikov, Ilya and Wilkins, Angela and Lichtarge, Olivier and Chi, Po-Han and Tseng, Wei-Cheng and Linial, Michal and Rose, Peter W. and Dessimoz, Christophe and Vidulin, Vedrana and Dzeroski, Saso and Sillitoe, Ian and Das, Sayoni and Lees, Jonathan Gill and Jones, David T. and Wan, Cen and Cozzetto, Domenico and Fa, Rui and Torres, Mateo and Warwick Vesztrocy, Alex and Rodriguez, Jose Manuel and Tress, Michael L. and Frasca, Marco and Notaro, Marco and Grossi, Giuliano and Petrini, Alessandro and Re, Matteo and Valentini, Giorgio and Mesiti, Marco and Roche, Daniel B. and Reeb, Jonas and Ritchie, David W. and Aridhi, Sabeur and Alborzi, Seyed Ziaeddin and Devignes, Marie-Dominique and Koo, Da Chen Emily and Bonneau, Richard and Gligorijevi\'{c}, Vladimir and Barot, Meet and Fang, Hai and Toppo, Stefano and Lavezzo, Enrico and Falda, Marco and Berselli, Michele and Tosatto, Silvio C.E. and Carraro, Marco and Piovesan, Damiano and Ur Rehman, Hafeez and Mao, Qizhong and Zhang, Shanshan and Vucetic, Slobodan and Black, Gage S. and Jo, Dane and Suh, Erica and Dayton, Jonathan B. and Larsen, Dallas J. and Omdahl, Ashton R. and McGuffin, Liam J. and Brackenridge, Danielle A. and Babbitt, Patricia C. and Yunes, Jeffrey M. and Fontana, Paolo and Zhang, Feng and Zhu, Shanfeng and You, Ronghui and Zhang, Zihan and Dai, Suyang and Yao, Shuwei and Tian, Weidong and Cao, Renzhi and Chandler, Caleb and Amezola, Miguel and Johnson, Devon and Chang, Jia-Ming and Liao, Wen-Hung and Liu, Yi-Wei and Pascarelli, Stefano and Frank, Yotam and Hoehndorf, Robert and Kulmanov, Maxat and Boudellioua, Imane and Politano, Gianfranco and Di Carlo, Stefano and Benso, Alfredo and Hakala, Kai and Ginter, Filip and Mehryary, Farrokh and Kaewphan, Suwisa and Bj\"{o}rne, Jari and Moen, Hans and Tolvanen, Martti E.E. and Salakoski, Tapio and Kihara, Daisuke and Jain, Aashish and \v{S}muc, Tomislav and Altenhoff, Adrian and Ben-Hur, Asa and Rost, Burkhard and Brenner, Steven E. and Orengo, Christine A. and Jeffery, Constance J. and Bosco, Giovanni and Hogan, Deborah A. and Martin, Maria J. and O’Donovan, Claire and Mooney, Sean D. and Greene, Casey S. and Radivojac, Predrag and Friedberg, Iddo}, year = {2019}, pages = {23}, DOI = {10.1186/s13059-019-1835-8}, chapter = {244}, keywords = {protein function prediction}, journal = {Genome Biology}, doi = {10.1186/s13059-019-1835-8}, volume = {20}, number = {1}, issn = {1474-760X}, title = {The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens}, keyword = {protein function prediction}, chapternumber = {244} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE

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