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PANTHER


NAR Molecular Biology Database Collection entry number 552

Database Description

PANTHER (Protein ANalysis THrough Evolutionary Relationships) relates protein sequence evolution to function evolution. Evolutionary relationships between sequences are represented by protein family trees, and these trees are annotated by expert biologists to reflect the divergence of function. Specific protein subfamilies are annotated with molecular function and biological process ontology terms, and are mapped to pathways. Trees (including multiple sequence alignments and biologist annotation) and detailed pathways can be viewed interactively on the web, or downloaded as data. We have also implemented web services for (1) protein sequence classification using subfamily Hidden Markov Models (HMMs), (2) analysis of mRNA or protein expression data using ontology and pathway classifications and pathway diagrams, and (3) scoring of nonsynonymous coding SNPs for likely functional effects using the HMMs and multiple sequence alignments.

Recent Developments

PANTHER Pathways now include a large number of expert curated pathways generated using the CellDesigner/SBML standard.

References

1. P.D. Thomas, M.J. Campbell, A. Kejariwal, H. Mi, B. Karlak, R. Daverman, K. Diemer, A. Muruganujan, A. Narechania. 2003. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res., 13: 2129-2141.
2. P.D. Thomas, A. Kejariwal, M.J. Campbell, H. Mi, K. Diemer, N. Guo, I. Ladunga, B. Ulitsky-Lazareva, A. Muruganujan, S. Rabkin, J.A. Vandergriff and O. Doremieux. 2003. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucl. Acids. Res. 31:3.34-341.


Go to the abstract in the NAR 2010 Database Issue.
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