PANTHER
| Content | |
|---|---|
| Description | The PANTHER database classifies gene products into families |
| Data types captured | Gene families |
| Contact | |
| Research center | University of Southern California |
| Authors | Paul D Thomas |
| Primary citation | PMID 12520017 |
| Access | |
| Website | [1] |
| Miscellaneous | |
| Bookmarkable entities | yes |
In bioinformatics the PANTHER (Protein ANalysis THrough Evolutionary Relationships) classification system is a biological database that can be used to classify and identify the function of gene products.[1] PANTHER is part of the Gene Ontology Reference Genome Project[2] designed to classify proteins and their genes for high-throughput analysis.
The project consists of both manual curation and bioinformatics algorithms.[3] Proteins are classified according to family (and subfamily), molecular function, biological process and pathway. It is one of the databases feeding into the European Bioinformatics Institute's InterPro database.[4]
PANTHER
Protein Analysis Through Evolutuonary Relationship (PANTHER) is a database aim to delivery high-throughput analysis of proteins sequences. One of the interesting feature of this PANTHER is that user can browse the database based on protein function. Another interesting feature of PANTHER db it draws protein sequence in pythalogic tree format for each sub-family.
PANTHER History
- 1998:Project was launched at Molecular Application Group.
- 1999:Acquired by Celera Genomics.
- 2000:PANTHER 1 released in Celera Discovery Systems (CDS).
- 2001: PANTHER 2 released, which is used in the annotationon of the first published human genome Celera.
- 2002: PANTHER 3 released. PANTHER annotations are integrated in FlyBase.Moved to ABI
- 2003: PANTHER 4 released with the public release of PANTHER Classification System.
- 2005: PANTHER 5 released with PANTHER Pathway and analysis tool.Establish collabora3on with Interpro.
- 2006: PANTHER 6 released. Move to SRI.
- 2010: PANTHER 7 released.
- 2011: Move to USC.
- 2012: PANTHER 8 released.
- 2014: PANTHER 9 released
Phylogenetic Tree
In panther there is a pythogenetic tree for each of the protein families. Each of the node in this tree is annotated gene attributes. This gene attribute depicts ‘subfamily membership’, ‘protein class’ and gene function. Intersting part of this tree functionality is that internal node also depicts evolutionary event i.e speciation, gene duplication, horizontal gene transfer. In addition to this tree are annoted with gene ontology(GO) terms. Gene ontology is part of reference genome project. To generate pythologic tree PANTHER uses GIGA algorithm. GIGA uses species tree to develop tree construction on every iterationit attemp to reconcile tree in event form of speciation, gene duplication
PANTHER Library Data Generation Process
The process for data generation is divided in three step
- Family Clustering
- Pythologentic Tree Building
- Annotation of Tree Nodes
External References
References
- ^ Thomas, PD.; Kejariwal, A.; Campbell, MJ.; Mi, H.; Diemer, K.; Guo, N.; Ladunga, I.; Ulitsky-Lazareva, B.; et al. (Jan 2003). "PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification". Nucleic Acids Res. 31 (1): 334–41. doi:10.1093/nar/gkg115. PMC 165562. PMID 12520017.
- ^ GO Reference Genome Annotation Project
- ^ Mi, H.; Muruganujan, A.; Thomas, PD. (Jan 2013). "PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees". Nucleic Acids Res. 41 (Database issue): D377–86. doi:10.1093/nar/gks1118. PMID 23193289.
- ^ Hunter, S.; Jones, P.; Mitchell, A.; Apweiler, R.; Attwood, TK.; Bateman, A.; Bernard, T.; Binns, D.; et al. (Jan 2012). "InterPro in 2011: new developments in the family and domain prediction database". Nucleic Acids Res. 40 (Database issue): D306–12. doi:10.1093/nar/gkr948. PMC 3245097. PMID 22096229.
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