Large-scale gene function analysis with the PANTHER classification system

doi:10.1038/nprot.2013.092

2013-07-18

2.2K

DOI：10.1038/nprot.2013.092

原文链接

原文求助

摘要

En 中文

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

Keyword:

GENOME-WIDE ASSOCIATION

PROTEIN FAMILIES

EVOLUTION

DATABASE

PATHWAY

IDENTIFICATION

SUBFAMILIES

SEQUENCE

LOCI

期刊

Nature Protocols

IF:

论文数:

4.0K

被引数:

5.6W

机构

university of southern california

学者数:

4.7W

论文数: 3.8W

被引数: 51

引用论文

Pathway Commons, a web resource for biological pathway data

NUCLEIC ACIDS RESEARCH

IF13.1

2010-11-10

626

OAAI

Cerami, Ethan G.; Gross, Benjamin E.; Demir, Emek; Rodchenkov, Igor; Babur, Oezguen; Anwar, Nadia; Schultz, Nikolaus; Bader, Gary D.; Sander, Chris

Gene expression profiling and pathway analysis identify the integrin signaling pathway to be altered by IL-1β in human pancreatic cancer cells: Role of JNK

CANCER LETTERS

IF10.1

2012-07-01

PREAI

Verma, Gaurav; Bhatia, Himanshi; Datta, Malabika

PANTHER: A library of protein families and subfamilies indexed by function PANTHER: 按功能索引的蛋白质家族和亚家族文库

GENOME RESEARCH

IF5.5

2003-09-02

2.7K

OAAI

Thomas, PD; Campbell, MJ; Kejariwal, A; Mi, HY; Karlak, B; Daverman, R; Diemer, K; Muruganujan, A; Narechania, A

Metastable polymorphs and luminescence of boehmite-derived alumina doped with divalent europium ions

Functional Materials Letters

IF0

2022-04-13

PREAI

Huirong Ma; Hongyang Zhao; Yuexin Song; Shan Liu; Zhiyong Mao; Dajian Wang

The BioPAX community standard for pathway data sharing

NATURE BIOTECHNOLOGY

IF41.7

2010-09-09

507

OAAI

Demir, Emek; Cary, Michael P.; Paley, Suzanne; Fukuda, Ken; Lemer, Christian; Vastrik, Imre; Wu, Guanming; D'Eustachio, Peter; Schaefer, Carl; Luciano, Joanne; Schacherer, Frank; Martinez-Flores, Irma; Hu, Zhenjun; Jimenez-Jacinto, Veronica; Joshi-Tope, Geeta; Kandasamy, Kumaran; Lopez-Fuentes, Alejandra C.; Mi, Huaiyu; Pichler, Elgar; Rodchenkov, Igor; Splendiani, Andrea; Tkachev, Sasha; Zucker, Jeremy; Gopinath, Gopal; Rajasimha, Harsha; Ramakrishnan, Ranjani; Shah, Imran; Syed, Mustafa; Anwar, Nadia; Babur, Oezguen; Blinov, Michael; Brauner, Erik; Corwin, Dan; Donaldson, Sylva; Gibbons, Frank; Goldberg, Robert; Hornbeck, Peter; Luna, Augustin; Murray-Rust, Peter; Neumann, Eric; Reubenacker, Oliver; Samwald, Matthias; van Iersel, Martijn; Wimalaratne, Sarala; Allen, Keith; Braun, Burk; Whirl-Carrillo, Michelle; Cheung, Kei-Hoi; Dahlquist, Kam; Finney, Andrew; Gillespie, Marc; Glass, Elizabeth; Gong, Li; Haw, Robin; Honig, Michael; Hubaut, Olivier; Kane, David; Krupa, Shiva; Kutmon, Martina; Leonard, Julie; Marks, Debbie; Merberg, David; Petri, Victoria; Pico, Alex; Ravenscroft, Dean; Ren, Liya; Shah, Nigam; Sunshine, Margot; Tang, Rebecca; Whaley, Ryan; Letovksy, Stan; Buetow, Kenneth H.; Rzhetsky, Andrey; Schachter, Vincent; Sobral, Bruno S.; Dogrusoz, Ugur; McWeeney, Shannon; Aladjem, Mirit; Birney, Ewan; Collado-Vides, Julio; Goto, Susumu; Hucka, Michael; Le Novere, Nicolas; Maltsev, Natalia; Pandey, Akhilesh; Thomas, Paul; Wingender, Edgar; Karp, Peter D.; Sander, Chris; Bader, Gary D.

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2003-01-14

522

OAAI

Mootha, VK; Lepage, P; Miller, K; Bunkenborg, J; Reich, M; Hjerrild, M; Delmonte, T; Villeneuve, A; Sladek, R; Xu, FH; Mitchell, GA; Morin, C; Mann, M; Hudson, TJ; Robinson, B; Rioux, JD; Lander, ES

Quantitative Proteomics with siRNA Screening Identifies Novel Mechanisms of Trastuzumab Resistance in HER2 Amplified Breast Cancers

MOLECULAR & CELLULAR PROTEOMICS

IF5.5

2013-01-01

OAAI

Boyer, Alaina P.; Collier, Timothy S.; Vidavsky, Ilan; Bose, Ron

Multiphoton effects in energy loss spectra

Physical Review D

IF0

1999-02-05

OAAI

V. N. Baier; V. M. Katkov

The Effect of Electron Irradiation on the Structure of Sodium Aluminum-Iron Phosphate Glasses 电子辐照对磷酸铝铁钠玻璃结构的影响

MRS Advances

IF0

2017-02-20

PREAI

S. V. Stefanovsky; O. I. Stefanovsky; M.I Kadyko; V. A. Zhachkin; L. D. Bogomolova

The Gene Ontology: enhancements for 2011

NUCLEIC ACIDS RESEARCH

IF13.1

2011-11-18

173

OAAI

Blake, J. A.; Dolan, M.; Drabkin, H.; Hill, D. P.; Ni, L.; Sitnikov, D.; Burgess, S.; Buza, T.; Gresham, C.; McCarthy, F.; Pillai, L.; Wang, H.; Carbon, S.; Lewis, S. E.; Mungall, C. J.; Gaudet, P.; Chisholm, R. L.; Fey, P.; Kibbe, W. A.; Basu, S.; Siegele, D. A.; McIntosh, B. K.; Renfro, D. P.; Zweifel, A. E.; Hu, J. C.; Brown, N. H.; Tweedie, S.; Alam-Faruque, Y.; Apweiler, R.; Auchinchloss, A.; Axelsen, K.; Argoud-Puy, G.; Bely, B.; Blatter, M. -C.; Bougueleret, L.; Boutet, E.; Branconi-Quintaje, S.; Breuza, L.; Bridge, A.; Browne, P.; Chan, W. M.; Coudert, E.; Cusin, I.; Dimmer, E.; Duek-Roggli, P.; Eberhardt, R.; Estreicher, A.; Famiglietti, L.; Ferro-Rojas, S.; Feuermann, M.; Gardner, M.; Gos, A.; Gruaz-Gumowski, N.; Hinz, U.; Hulo, C.; Huntley, R.; James, J.; Jimenez, S.; Jungo, F.; Keller, G.; Laiho, K.; Legge, D.; Lemercier, P.; Lieberherr, D.; Magrane, M.; Martin, M. J.; Masson, P.; Moinat, M.; O'Donovan, C.; Pedruzzi, I.; Pichler, K.; Poggioli, D.; Millan, P. Porras; Poux, S.; Rivoire, C.; Roechert, B.; Sawford, T.; Schneider, M.; Sehra, H.; Stanley, E.; Stutz, A.; Sundaram, S.; Tognolli, M.; Xenarios, I.; Foulger, R.; Lomax, J.; Roncaglia, P.; Camon, E.; Khodiyar, V. K.; Lovering, R. C.; Talmud, P. J.; Chibucos, M.; Giglio, M. Gwinn; Dolinski, K.; Heinicke, S.; Livstone, M. S.; Stephan, R.; Harris, M. A.; Oliver, S. G.; Rutherford, K.; Wood, V.; Bahler, J.; Lock, A.; Kersey, P. J.; McDowall, M. D.; Staines, D. M.; Dwinell, M.; Shimoyama, M.; Laulederkind, S.; Hayman, T.; Wang, S. -J.; Petri, V.; Lowry, T.; D'Eustachio, P.; Matthews, L.; Amundsen, C. D.; Balakrishnan, R.; Binkley, G.; Cherry, J. M.; Christie, K. R.; Costanzo, M. C.; Dwight, S. S.; Engel, S. R.; Fisk, D. G.; Hirschman, J. E.; Hitz, B. C.; Hong, E. L.; Karra, K.; Krieger, C. J.; Miyasato, S. R.; Nash, R. S.; Park, J.; Skrzypek, M. S.; Weng, S.; Wong, E. D.; Berardini, T. Z.; Li, D.; Huala, E.; Slonim, D.; Wick, H.; Thomas, P.; Chan, J.; Kishore, R.; Sternberg, P.; Van Auken, K.; Howe, D.; Westerfield, M.

查看更多内容