RT Journal
A1 Thomas, Paul D.
A1 Campbell, Michael J.
A1 Kejariwal, Anish
A1 Mi, Huaiyu
A1 Karlak, Brian
A1 Daverman, Robin
A1 Diemer, Karen
A1 Muruganujan, Anushya
A1 Narechania, Apurva
T1 PANTHER: A Library of Protein Families and Subfamilies Indexed by Function
JF Genome Research 
JO Genome Research 
YR 2003 
FD September 01 
VO 13 
IS 9 
SP 2129 
OP 2141 
DO 10.1101/gr.772403 
UL http://genome.cshlp.org/content/13/9/2129.abstract 
AB 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.