g:Profiler-interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)

被引:529
作者
Kolberg, Liis [1 ]
Raudvere, Uku [1 ]
Kuzmin, Ivan [1 ]
Adler, Priit [1 ]
Vilo, Jaak [1 ,2 ]
Peterson, Hedi [1 ]
机构
[1] Univ Tartu, Inst Comp Sci, Narva mnt 18, EE-51009 Tartu, Estonia
[2] Software Technol & Applicat Competence Ctr, Narva mnt 20, EE-51009 Tartu, Estonia
关键词
RESOURCE; LISTS; TOOL;
D O I
10.1093/nar/gkad347
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
g:Profiler is a reliable and up-to-date functional enrichment analysis tool that supports various evidence types, identifier types and organisms. The toolset integrates many databases, including Gene Ontology, KEGG and TRANSFAC, to provide a comprehensive and in-depth analysis of gene lists. It also provides interactive and intuitive user interfaces and supports ordered queries and custom statistical backgrounds, among other settings. g:Profiler provides multiple programmatic interfaces to access its functionality. These can be easily integrated into custom workflows and external tools, making them valuable resources for researchers who want to develop their own solutions. g:Profiler has been available since 2007 and is used to analyse millions of queries. Research reproducibility and transparency are achieved by maintaining working versions of all past database releases since 2015. g:Profiler supports 849 species, including vertebrates, plants, fungi, insects and parasites, and can analyse any organism through user-uploaded custom annotation files. In this update article, we introduce a novel filtering method highlighting Gene Ontology driver terms, accompanied by new graph visualizations providing a broader context for significant Gene Ontology terms. As a leading enrichment analysis and gene list interoperability service, g:Profiler offers a valuable resource for genetics, biology and medical researchers. It is freely accessible at https://biit.cs.ut.ee/gprofiler. [GRAPHICS] .
引用
收藏
页码:W207 / W212
页数:6
相关论文
共 27 条
[1]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[2]   The Gene Ontology resource: enriching a GOld mine [J].
Carbon, Seth ;
Douglass, Eric ;
Good, Benjamin M. ;
Unni, Deepak R. ;
Harris, Nomi L. ;
Mungall, Christopher J. ;
Basu, Siddartha ;
Chisholm, Rex L. ;
Dodson, Robert J. ;
Hartline, Eric ;
Fey, Petra ;
Thomas, Paul D. ;
Albou, Laurent-Philippe ;
Ebert, Dustin ;
Kesling, Michael J. ;
Mi, Huaiyu ;
Muruganujan, Anushya ;
Huang, Xiaosong ;
Mushayahama, Tremayne ;
LaBonte, Sandra A. ;
Siegele, Deborah A. ;
Antonazzo, Giulia ;
Attrill, Helen ;
Brown, Nick H. ;
Garapati, Phani ;
Marygold, Steven J. ;
Trovisco, Vitor ;
Dos Santos, Gil ;
Falls, Kathleen ;
Tabone, Christopher ;
Zhou, Pinglei ;
Goodman, Joshua L. ;
Strelets, Victor B. ;
Thurmond, Jim ;
Garmiri, Penelope ;
Ishtiaq, Rizwan ;
Rodriguez-Lopez, Milagros ;
Acencio, Marcio L. ;
Kuiper, Martin ;
Laegreid, Astrid ;
Logie, Colin ;
Lovering, Ruth C. ;
Kramarz, Barbara ;
Saverimuttu, Shirin C. C. ;
Pinheiro, Sandra M. ;
Gunn, Heather ;
Su, Renzhi ;
Thurlow, Katherine E. ;
Chibucos, Marcus ;
Giglio, Michelle .
NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D325-D334
[3]   Ensembl 2022 [J].
Cunningham, Fiona ;
Allen, James E. ;
Allen, Jamie ;
Alvarez-Jarreta, Jorge ;
Amode, M. Ridwan ;
Armean, Irina M. ;
Austine-Orimoloye, Olanrewaju ;
Azov, Andrey G. ;
Barnes, If ;
Bennett, Ruth ;
Berry, Andrew ;
Bhai, Jyothish ;
Bignell, Alexandra ;
Billis, Konstantinos ;
Boddu, Sanjay ;
Brooks, Lucy ;
Charkhchi, Mehrnaz ;
Cummins, Carla ;
Fioretto, Luca Da Rin ;
Davidson, Claire ;
Dodiya, Kamalkumar ;
Donaldson, Sarah ;
El Houdaigui, Bilal ;
El Naboulsi, Tamara ;
Fatima, Reham ;
Giron, Carlos Garcia ;
Genez, Thiago ;
Martinez, Jose Gonzalez ;
Guijarro-Clarke, Cristina ;
Gymer, Arthur ;
Hardy, Matthew ;
Hollis, Zoe ;
Hourlier, Thibaut ;
Hunt, Toby ;
Juettemann, Thomas ;
Kaikala, Vinay ;
Kay, Mike ;
Lavidas, Ilias ;
Le, Tuan ;
Lemos, Diana ;
Marugan, Jose Carlos ;
Mohanan, Shamika ;
Mushtaq, Aleena ;
Naven, Marc ;
Ogeh, Denye N. ;
Parker, Anne ;
Parton, Andrew ;
Perry, Malcolm ;
Pilizota, Ivana ;
Prosovetskaia, Irina .
NUCLEIC ACIDS RESEARCH, 2022, 50 (D1) :D988-D995
[4]   The reactome pathway knowledgebase 2022 [J].
Gillespie, Marc ;
Jassal, Bijay ;
Stephan, Ralf ;
Milacic, Marija ;
Rothfels, Karen ;
Senff-Ribeiro, Andrea ;
Griss, Johannes ;
Sevilla, Cristoffer ;
Matthews, Lisa ;
Gong, Chuqiao ;
Deng, Chuan ;
Varusai, Thawfeek ;
Ragueneau, Eliot ;
Haider, Yusra ;
May, Bruce ;
Shamovsky, Veronica ;
Weiser, Joel ;
Brunson, Timothy ;
Sanati, Nasim ;
Beckman, Liam ;
Shao, Xiang ;
Fabregat, Antonio ;
Sidiropoulos, Konstantinos ;
Murillo, Julieth ;
Viteri, Guilherme ;
Cook, Justin ;
Shorser, Solomon ;
Bader, Gary ;
Demir, Emek ;
Sander, Chris ;
Haw, Robin ;
Wu, Guanming ;
Stein, Lincoln ;
Hermjakob, Henning ;
D'Eustachio, Peter .
NUCLEIC ACIDS RESEARCH, 2022, 50 (D1) :D687-D692
[5]   WormBase ParaSite - a comprehensive resource for helminth genomics [J].
Howe, Kevin L. ;
Bolt, Bruce J. ;
Shafie, Myriam ;
Kersey, Paul ;
Berriman, Matthew .
MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 2017, 215 :2-10
[6]   WormBase 2016: expanding to enable helminth genomic research [J].
Howe, Kevin L. ;
Bolt, Bruce J. ;
Cain, Scott ;
Chan, Juancarlos ;
Chen, Wen J. ;
Davis, Paul ;
Done, James ;
Down, Thomas ;
Gao, Sibyl ;
Grove, Christian ;
Harris, Todd W. ;
Kishore, Ranjana ;
Lee, Raymond ;
Lomax, Jane ;
Li, Yuling ;
Muller, Hans-Michael ;
Nakamura, Cecilia ;
Nuin, Paulo ;
Paulini, Michael ;
Raciti, Daniela ;
Schindelman, Gary ;
Stanley, Eleanor ;
Tuli, Mary Ann ;
Van Auken, Kimberly ;
Wang, Daniel ;
Wang, Xiaodong ;
Williams, Gary ;
Wright, Adam ;
Yook, Karen ;
Berriman, Matthew ;
Kersey, Paul ;
Schedl, Tim ;
Stein, Lincoln ;
Sternberg, Paul W. .
NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D774-D780
[7]   miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions [J].
Huang, Hsi-Yuan ;
Lin, Yang-Chi-Dung ;
Cui, Shidong ;
Huang, Yixian ;
Tang, Yun ;
Xu, Jiatong ;
Bao, Jiayang ;
Li, Yulin ;
Wen, Jia ;
Zuo, Huali ;
Wang, Weijuan ;
Li, Jing ;
Ni, Jie ;
Ruan, Yini ;
Li, Liping ;
Chen, Yidan ;
Xie, Yueyang ;
Zhu, Zihao ;
Cai, Xiaoxuan ;
Chen, Xinyi ;
Yao, Lantian ;
Chen, Yigang ;
Luo, Yijun ;
LuXu, Shupeng ;
Luo, Mengqi ;
Chiu, Chih-Min ;
Ma, Kun ;
Zhu, Lizhe ;
Cheng, Gui-Juan ;
Bai, Chen ;
Chiang, Ying-Chih ;
Wang, Liping ;
Wei, Fengxiang ;
Lee, Tzong-Yi ;
Huang, Hsien-Da .
NUCLEIC ACIDS RESEARCH, 2022, 50 (D1) :D222-D230
[8]   KEGG for taxonomy-based analysis of pathways and genomes [J].
Kanehisa, Minoru ;
Furumichi, Miho ;
Sato, Yoko ;
Kawashima, Masayuki ;
Ishiguro-Watanabe, Mari .
NUCLEIC ACIDS RESEARCH, 2023, 51 (D1) :D587-D592
[9]   The Human Phenotype Ontology in 2021 [J].
Koehler, Sebastian ;
Gargano, Michael ;
Matentzoglu, Nicolas ;
Carmody, Leigh C. ;
Lewis-Smith, David ;
Vasilevsky, Nicole A. ;
Danis, Daniel ;
Balagura, Ganna ;
Baynam, Gareth ;
Brower, Amy M. ;
Callahan, Tiffany J. ;
Chute, Christopher G. ;
Est, Johanna L. ;
Galer, Peter D. ;
Ganesan, Shiva ;
Griese, Matthias ;
Haimel, Matthias ;
Pazmandi, Julia ;
Hanauer, Marc ;
Harris, Nomi L. ;
Hartnett, Michael J. ;
Hastreiter, Maximilian ;
Hauck, Fabian ;
He, Yongqun ;
Jeske, Tim ;
Kearney, Hugh ;
Kindle, Gerhard ;
Klein, Christoph ;
Knoflach, Katrin ;
Krause, Roland ;
Lagorce, David ;
McMurry, Julie A. ;
Miller, Jillian A. ;
Munoz-Torres, Monica C. ;
Peters, Rebecca L. ;
Rapp, Christina K. ;
Rath, Ana M. ;
Rind, Shahmir A. ;
Rosenberg, Avi Z. ;
Segal, Michael M. ;
Seidel, Markus G. ;
Smedley, Damian ;
Talmy, Tomer ;
Thomas, Yarlalu ;
Wiafe, Samuel A. ;
Xian, Julie ;
Yueksel, Zafer ;
Helbig, Ingo ;
Mungall, Christopher J. ;
Haendel, Melissa A. .
NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D1207-D1217
[10]  
Kolberg Liis, 2020, F1000Res, V9, DOI 10.12688/f1000research.24956.1