Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

Nature Protocols
Huaiyu MiPaul D Thomas

Abstract

The PANTHER classification system ( http://www.pantherdb.org ) is a comprehensive system that combines genomes, gene function classifications, pathways and statistical analysis tools to enable biologists to analyze large-scale genome-wide experimental data. The current system (PANTHER v.14.0) covers 131 complete genomes organized into gene families and subfamilies; evolutionary relationships between genes are represented in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models (HMMs)). The families and subfamilies are annotated with Gene Ontology (GO) terms, and sequences are assigned to PANTHER pathways. A suite of tools has been built to allow users to browse and query gene functions and analyze large-scale experimental data with a number of statistical tests. PANTHER is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. Since the protocol for using this tool (v.8.0) was originally published in 2013, there have been substantial improvements and updates in the areas of data quality, data coverage, statistical algorithms and user experience. This Protocol Update provides detailed instructions on how to analyze genome-wide experimental data in t...Continue Reading

References

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Citations

Mar 5, 2020·EMBO Molecular Medicine·Cristian Prieto-GarciaMarkus E Diefenbacher
Mar 5, 2020·Stem Cells·Zhilin MaWei Du
Feb 7, 2020·G3 : Genes - Genomes - Genetics·Elizabeth B BrownStephanie M Rollmann
Apr 14, 2020·Chembiochem : a European Journal of Chemical Biology·Jim VoorneveldDmitri V Filippov
Oct 31, 2019·Genetics, Selection, Evolution : GSE·Ina HulseggeKor Oldenbroek
Jun 14, 2020·International Journal of Molecular Sciences·Julia PanovHanoch Kaphzan
Jul 2, 2020·Nucleic Acids Research·Judhajeet RayJohn T Lis
May 20, 2020·Bioinformatics·Christopher J NeelyBenjamin J Tully
Aug 20, 2020·PloS One·Dina A El-KhishinMohamed I Abouelhoda
Aug 26, 2020·Acta Neuropathologica·Aivi T NguyenEdward B Lee
Sep 10, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Hanna DanielewiczAndrzej Boznański
Aug 11, 2020·Reproduction in Domestic Animals = Zuchthygiene·Firdous A KhanTracey S Chenier
Oct 1, 2020·Cellular and Molecular Life Sciences : CMLS·Bi ZhaoLukasz Kurgan
Sep 6, 2019·G3 : Genes - Genomes - Genetics·Diep R GangulyBarry J Pogson
Jan 5, 2020·BMC Research Notes·Manon RuffinLoic Guillot
Mar 15, 2020·Journal of Molecular Neuroscience : MN·Rajaneekar DasariSangeetha Sukumari-Ramesh
Mar 25, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Camille Lombard-Banek, John E Schiel
May 13, 2020·Cells·Ida Sofie GrønningsæterKimberley Joanne Hatfield
May 28, 2020·Journal of Clinical Medicine·Lilach SimchiHanoch Kaphzan

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Methods Mentioned

BETA
pull-down

Software Mentioned

Windows 7
HMMER
Perl
Reactome
PANTHER Scoring Tool
MacOS
hmmscan
Safari
UniProt
Windows XP

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