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

Nature Protocols volume 14, pages 703–721 (2019)Cite this article

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 the PANTHER classification system.

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Fig. 1: Overview of PANTHER infrastructure and recent improvements.
Fig. 2: The PANTHER home page with the gene list analysis tools.
Fig. 3: Results of functional classification displayed as a gene list page.
Fig. 4: Graphical PANTHER results.
Fig. 5: User interface of the statistical over-representation test, allowing the user to configure the analysis criteria.
Fig. 6: Result from the statistical over-representation test.
Fig. 7: The results from the statistical enrichment test.
Fig. 8: Graph of the results from the enrichment test.

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Code availability

Source codes for various PANTHER software, including the PANTHER scoring tool, and the tree-building tool (GIGA), can be downloaded at http://www.pantherdb.org/downloads/index.jsp.

Data availability

All PANTHER data are publicly available and can be downloaded at http://www.pantherdb.org/downloads/index.jsp.

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Acknowledgements

The authors thank the InterPro team, especially L. Richardson and R. Finn, for their support in providing PANTHER matching files used to generate PANTHER Generic Mapping files; the Reference Proteome team, especially M. Martin, for their support in providing up-to-date Reference Proteome datasets; the Gene Ontology Consortium, especially P. Gaudet, M. Feuermann and S. Lewis, for their support in providing GO phylogenetic annotation data; and the Reactome team, especially R. Haw, for their support in providing the Reactome dataset. The authors also thank A. Toga and the BDDS (Big Data for Discovery Science) Project for providing the funding to develop the software for supporting genetic variant analysis. This work is supported by NIH/NHGRI U41HG002273 and NSF 1458808 to P.D.T., and NIH U54EB020406 to A. Toga. Funding for open-access charge: University of Southern California.

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Author notes

  1. Xiaosong Huang

    Present address: School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China

Authors and Affiliations

  1. Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

    Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Dustin Ebert, Caitlin Mills, Xinyu Guo & Paul D. Thomas

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  1. Huaiyu Mi
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Contributions

A.M. developed the software code for the website. X.H. generated the content of the PANTHER database and provided administrative support to maintain the database. D.E. built the current PANTHER release (v.14.0). C.M. developed the workflow to integrate Reactome data into the analysis. X.G. helped in the development and implementation of Fisher’s exact test in PANTHER. H.M. developed the new process to generate the PANTHER Generic Mapping file, and supervised the project. P.D.T. provided funding and supervised the project. H.M. wrote the manuscript, with contributions from all other authors.

Corresponding authors

Correspondence to Huaiyu Mi or Paul D. Thomas.

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The authors declare no competing interests.

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Key references using this protocol

Mi, H., Muruganujan, A., Ebert, D., Huang, X. & Thomas, P. D. Nucleic Acids Res. 47, D419–D426 (2019): https://doi.org/10.1093/nar/gky1038

The Gene Ontology Consortium. Nucleic Acids Res. 45, D331–D338 (2017): https://doi.org/10.1093/nar/gkw1108

Mi, H. & Thomas, P. Methods Mol. Biol. 563, 123–140 (2009): https://doi.org/10.1007/978-1-60761-175-2_7

Protocol update to:

Mi, H., Muruganujan, A., Casagrande, J. T. & Thomas, P. D. Nat. Protoc. 8, 1551–1566 (2013): https://doi.org/10.1038/nprot.2013.092

This protocol is an update to Nat. Protoc. 8, 1551–1566 (2013): https://doi.org/10.1038/nprot.2013.092

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Mi, H., Muruganujan, A., Huang, X. et al. Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat Protoc 14, 703–721 (2019). https://doi.org/10.1038/s41596-019-0128-8

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