The PANTHER database of protein families, subfamilies, functions and pathways

By Huaiyu Mi, Betty Lazareva-Ulitsky, R. Loo, Anish Kejariwal, Jody A. Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell and 2 more. Nucleic Acids Res., 2004

855 citations recorded by the source corpus.

PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathways), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. The latest version, 5.0, contains 6683 protein families, divided into 31 705 subfamilies, covering ∼90% of mammalian protein-coding genes. PANTHER 5.0 includes a number of significant improvements over previous versions, most notably (i) representation of pathways (primarily signaling pathways) and association with subfamilies and individual protein sequences; (ii) an improved methodology for defining the PANTHER families and subfamilies, and for building the HMMs; (iii) resources for scoring sequences against PANTHER HMMs both over the web and locally; and (iv) a number of new web resources to facilitate analysis of large gene lists, including data generated from high-throughput expression experiments. Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com.

Subfields: Molecular Biology

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Citations in the corpus

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system (2016, methodology): “Genome-speciﬁc metabolic potential was determined by (1) searching all predicted ORFs in a genome with Pfam 35 , TIGRfam 34 , Panther 69 and custom HMM proﬁles (Supplementary Data 8 and 12) of marker genes for speciﬁc pathways using hmmscan 36 , and (2) assessment of complete pathways for metabolic…”
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells (2006, background): “All the distinct genes associated with the binding sites were further annotated with the Panther classification syste”
Using process diagrams for the graphical representation of biological networks (2005, methodology): “The pathway modules in PANTHER service by Applied Biosystems is an example of extensive use of the notation and CellDesigner software by a third party, and has been shown to be effective 14 .”
Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. (2008, methodology): “…Analyses Sets of hit genes were classified into functional categories such as biological process, molecular function (PANTHER classification system) (Mi et al., 2005), canonical pathways (MSigDB) (Subramanian et al., 2005), and transcription factor (TF)-binding sites (MSigDB and TRANSFAC v7.”
Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools (2006, methodology): “The PANTHER database (1,2) was designed to model the relationships between protein sequence and function for all major protein families, using molecular taxonomy tree building combined with human biological interpretation of the resulting trees.”
Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. (2006, methodology): “Gene ontology (GO) analysis was facilitated by PANTHER software ( 28 ).11 Selected gene lists”
Reactome: a knowledge base of biologic pathways and processes (2007, background): “Panther Pathways [36,37] is a curated collection of human pathways with an emphasis on signaling.”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, background): “12 While GO biological process terms include pathways, computational pathway representations provide additional information not found in traditional GO annotations: the ordering and dependencies of the individual protein functions within the pathway (Figure 1).”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, positive): “The InterPro consortium integrates databases of protein families, domains and functional sites, including: Gene3D (30), PANTHER (31), Pfam (32), PIRSF (33), PRINTS (34), ProDom (35), PROSITE (36), SMART (37), SUPERFAMILY and TIGRFAMs (38).”
TreeFam: a curated database of phylogenetic trees of animal gene families (2005, methodology): “Protein classification databases such as PANTHER (12) and SYSTERS (13) define families according to the degree of similarity between family members.”
Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus (2012, positive): “PANTHER database (Mi et al., 2005) was used to determine the protein class distribution of annotated transcripts and protein sequences in primary Tupaia hepatocytes (PTHs) generated in this study and transcriptome from primary human hepatocytes (PHHs) reported by Hart et al.”
Large-scale gene function analysis with PANTHER Classification System (2013, methodology): “In 2005, we began providing annotations of biochemical pathways, which can be viewed via the new PANTHER pathway applet 6,7 .”
New developments in the InterPro database (2007, methodology): “Two new member databases have been integrated into InterPro, PANTHER and Gene3D.”
InterProScan: protein domains identifier (2005, background): “ProDom (6) BlastProDom (Blastall) (4) PRINTS (7) FingerPrintScan (8) SMART (9) Hmmpfam (http://hmmer.wustl.edu/) TIGRFAMs (10) Hmmpfam (http://hmmer.wustl.edu/) Pfam (11) Hmmpfam (http://hmmer.wustl.edu/) PROSITE (12) ScanRegExp + ProfileScan (13) PIRSF (14) Hmmpfam (http://hmmer.wustl.edu/) SUPERFA”