PANTHER: a library of protein families and subfamilies indexed by function
- PMID: 12952881
- PMCID: PMC403709
- DOI: 10.1101/gr.772403
PANTHER: a library of protein families and subfamilies indexed by function
Abstract
In the genomic era, one of the fundamental goals is to characterize the function of proteins on a large scale. We describe a method, PANTHER, for relating protein sequence relationships to function relationships in a robust and accurate way. PANTHER is composed of two main components: the PANTHER library (PANTHER/LIB) and the PANTHER index (PANTHER/X). PANTHER/LIB is a collection of "books," each representing a protein family as a multiple sequence alignment, a Hidden Markov Model (HMM), and a family tree. Functional divergence within the family is represented by dividing the tree into subtrees based on shared function, and by subtree HMMs. PANTHER/X is an abbreviated ontology for summarizing and navigating molecular functions and biological processes associated with the families and subfamilies. We apply PANTHER to three areas of active research. First, we report the size and sequence diversity of the families and subfamilies, characterizing the relationship between sequence divergence and functional divergence across a wide range of protein families. Second, we use the PANTHER/X ontology to give a high-level representation of gene function across the human and mouse genomes. Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function.
Figures
![Figure 1](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f1_L1TT.gif)
![Figure 2](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f2_L1TT.gif)
![Figure 3](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f3_L1TT_rev1.gif)
![Figure 4](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f4a_L1TT.gif)
![Figure 4](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f4a_L1TT.gif)
![Figure 5](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f5_L1TT_rev1.gif)
![Figure 6](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f6_F4TT.gif)
![Figure 7](https://cdn.statically.io/img/www.ncbi.nlm.nih.gov/pmc/articles/instance/403709/bin/66468-14f7_F4TT.gif)
Similar articles
-
PANTHER: Making genome-scale phylogenetics accessible to all.Protein Sci. 2022 Jan;31(1):8-22. doi: 10.1002/pro.4218. Epub 2021 Nov 25. Protein Sci. 2022. PMID: 34717010 Free PMC article. Review.
-
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.Nucleic Acids Res. 2007 Jan;35(Database issue):D247-52. doi: 10.1093/nar/gkl869. Epub 2006 Nov 27. Nucleic Acids Res. 2007. PMID: 17130144 Free PMC article.
-
The PANTHER database of protein families, subfamilies, functions and pathways.Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8. doi: 10.1093/nar/gki078. Nucleic Acids Res. 2005. PMID: 15608197 Free PMC article.
-
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.Nucleic Acids Res. 2003 Jan 1;31(1):334-41. doi: 10.1093/nar/gkg115. Nucleic Acids Res. 2003. PMID: 12520017 Free PMC article.
-
Profile hidden Markov models.Bioinformatics. 1998;14(9):755-63. doi: 10.1093/bioinformatics/14.9.755. Bioinformatics. 1998. PMID: 9918945 Review.
Cited by
-
The Long Non-Coding RNA MALAT1 Modulates NR4A1 Expression through a Downstream Regulatory Element in Specific Cancer Cell Types.Int J Mol Sci. 2024 May 18;25(10):5515. doi: 10.3390/ijms25105515. Int J Mol Sci. 2024. PMID: 38791553 Free PMC article.
-
In vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis.Commun Biol. 2024 May 24;7(1):628. doi: 10.1038/s42003-024-06340-0. Commun Biol. 2024. PMID: 38789612 Free PMC article.
-
Integrated proteomic, phosphoproteomic, and N-glycoproteomic analyses of small extracellular vesicles from C2C12 myoblasts identify specific PTM patterns in ligand-receptor interactions.Cell Commun Signal. 2024 May 16;22(1):273. doi: 10.1186/s12964-024-01640-8. Cell Commun Signal. 2024. PMID: 38755675 Free PMC article.
-
Lactobacillus paracasei subsp. paracasei 2004 improves health and lifespan in Caenorhabditis elegans.Sci Rep. 2024 May 7;14(1):10453. doi: 10.1038/s41598-024-60580-y. Sci Rep. 2024. PMID: 38714725 Free PMC article.
-
Chromatin accessibility profiling reveals that human fibroblasts respond to mechanical stimulation in a cell-specific manner.JBMR Plus. 2024 Feb 29;8(5):ziae025. doi: 10.1093/jbmrpl/ziae025. eCollection 2024 May. JBMR Plus. 2024. PMID: 38682000 Free PMC article.
References
WEB SITE REFERENCES
-
- ftp://ftp.ncbi.nih.gov/refseq/LocusLink/; NCBI LocusLink.
-
- http://panther.celera.com; PANTHER Protein Classification.
-
- http://www.geneontology.org; Gene Ontology Consortium.
-
- http://www.ncbi.nlm.nih.gov/omim/; OMIM, Online Mendelian Inheritance in Man.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources