PANTHER: a library of protein families and subfamilies indexed by function.

By Paul D. Thomas, Michael J. Campbell, Anish Kejariwal, Huaiyu Mi, Brian Karlak, R. Daverman, Karen Diemer, Anushya Muruganujan, A. Narechania. Genome Research, 2003

2,961 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f25e3f21bf3cd90f1d91816a9544dbeb2fe1af12

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Citations in the corpus

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API (2020, methodology): “PANTHER PC (originally called PANTHER/X) was designed as a simple, high-level classification of the functions of proteins and protein families (1).”
dbNSFP: A Lightweight Database of Human Non-synonymous SNPs and Their Functional Predictions (2011, methodology): “, 2006] and PANTHER [Thomas et al., 2003], and building a fully functional Webserver for on-line database query.”
Predicting the Functional Effect of Amino Acid Substitutions and Indels (2012, methodology): “A number of computational methods have been developed based on such evolutionary principles to predict the effect of coding variants on protein function, including SIFT [5], PolyPhen-2 [6], Mutation Assessor [7], MAPP [8], PANTHER [9], LogR.”
FlyBase: genes and gene models (2004, background): “sg/dedb), PANTHERProtein Classification (11,12), Fly GRID Interaction Data (13), Hybrigenics PIMRider interactions (14), Interactive Fly (15), Yale Developmental Gene Expression (16) and NCBI’s Gene Expression Omnibus (17).”
The PANTHER database of protein families, subfamilies, functions and pathways (2004, methodology): “0, we implemented a number of improvements to the PANTHER library building procedure as described previously (1).”
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution (2010, positive): “Additionally, we performed pathway analyses using the PANTHER database 23 based on the same set of 95 genes (Online Methods and Supplementary Note).”
IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype (2012, background): “05 were considered as significantly over-represented in our gene list”
A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. (2009, positive): “Using PANTHER ( Thomas et al., 2003 ), we identified several biological processes including”
A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci (2008, neutral): “org/)[60].”
A Protein Complex Network of Drosophila melanogaster (2011, methodology): “Comparison of protein functional class distribution using the PANTHER classification system (Thomas et al., 2003) indicates that the distribution of protein categories of baits used and proteins identified in coAP-MS is very similar to the overall distribution of the Drosophila proteome, much of whi”
Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models (2012, methodology): “Here,wecompare ourunweighted methodagainstSIFTandPANTHER( A )whereas ourweighted method is compared to SNPs&GO and MutPred ( B ).”
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations (2014, background): “PANTHER was not able to evaluate 45% of the dataset mainly due to the fact that the investigated mutations could not be found at given positions in the pre-computed multiple sequence alignments of PANTHER library [54].”
Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “Although it initially aimed to classify gene and protein functions 2,3 , this system has evolved through the years to also serve as an online resource for analyzing experimental data 4 .”
Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools (2006, methodology): “Another use of statistical models of protein families and subfamilies is in assessing the likely functional effects of non-synonymous single-nucleotide polymorphisms (nsSNPs) (1,10).”