Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jan 1;33(Database issue):D284-8.
doi: 10.1093/nar/gki078.

The PANTHER database of protein families, subfamilies, functions and pathways

Huaiyu Mi  1 , Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J Campbell, Hiroaki Kitano, Paul D Thomas
Affiliations

The PANTHER database of protein families, subfamilies, functions and pathways

Huaiyu Mi et al. Nucleic Acids Res. .

Abstract

PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathways), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. The latest version, 5.0, contains 6683 protein families, divided into 31,705 subfamilies, covering approximately 90% of mammalian protein-coding genes. PANTHER 5.0 includes a number of significant improvements over previous versions, most notably (i) representation of pathways (primarily signaling pathways) and association with subfamilies and individual protein sequences; (ii) an improved methodology for defining the PANTHER families and subfamilies, and for building the HMMs; (iii) resources for scoring sequences against PANTHER HMMs both over the web and locally; and (iv) a number of new web resources to facilitate analysis of large gene lists, including data generated from high-throughput expression experiments. Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com.

PubMed Disclaimer

Figures

Figure 1
Figure 1
CellDesigner (6) diagram of the insulin/IGF receptor signaling pathway. Proteins (blue and brown boxes) are mapped onto PANTHER HMMs. Active forms (dashed-line boxes) and phosphorylated forms (small circles around the letter ‘P’) of proteins are clearly indicated in the diagram. Over 60 pathways (mostly signaling pathways) are currently available.
Figure 2
Figure 2
Statistical analysis of gene expression experiment results for a liver cancer versus normal cell line. Users can upload a list of genes/transcripts, along with an associated value (e.g. fold change, but can be any continuous variable). The list is divided automatically into groups sharing the same function (molecular function, biological process or pathway), and the distribution of values for each group is compared statistically with the overall distribution using the Mann–Whitney U-test to look for coordinated changes across each group (10).
Figure 3
Figure 3
Pie chart of molecular functions represented in a list of genes. Users can upload protein IDs to the PANTHER website, and pie charts can be drawn from any list.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Thomas P.D., Campbell,M.C., Kejariwal,A., Mi,H., Karlak,B., Daveran,R., Diemer,K., Muruganujan,A. and Narechania,A. (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res., 13, 2129–2141. - PMC - PubMed
    1. Thomas P.D., Kejariwal,A., Campbell,M.C., Mi,H., Diemer,K., Guo,N., Ladunga,I., Ulitsky-Lazareva,B., Muruganujan,A. and Rabkin,S. (2003) PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res., 31, 334–341. - PMC - PubMed
    1. Thomas P.D., Campbell,M.C., Kejariwal,A., Mi,H., Karlak,B., Daveran,R., Diemer,K., Muruganujan,A. and Narechania,A. (2003) Corrigendum for PANTHER: a library of protein families and subfamilies indexed by function. Nucleic Acids Res., 31, 2024. - PMC - PubMed
    1. Pruitt K.D. and Maglott,D.R. (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137–140. - PMC - PubMed
    1. FlyBase Consortium (2002) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res., 30, 106–108. - PMC - PubMed
-