PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

By Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas. Nucleic Acids Res., 2006

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PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles. Since 2005, there have been three main improvements to PANTHER. First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information. Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distributed as part of InterProScan. Third, we have dramatically expanded the number of pathways associated with subfamilies in PANTHER. Pathways provide a detailed, structured representation of protein function in the context of biological reaction networks. PANTHER pathways were generated using the emerging Systems Biology Markup Language (SBML) standard using pathway network editing software called CellDesigner. The pathway collection currently contains ∼1500 reactions in 130 pathways, curated by expert biologists with authorship attribution. The curation environment is designed to be easy to use, and the number of pathways is growing steadily. Because the reaction participants are linked to subfamilies and corresponding HMMs, reactions can be inferred across numerous different organisms. The HMMs can be downloaded by FTP, and tools for analyzing data in the context of pathways and function ontologies are available at .

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/016b106b7fa62a02bb2fb9b60f24b984adfe6918

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Citations in the corpus

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, neutral): “The inference approaches fall into two main categories, namely graph-based (8–15) and tree-based (16–19) methods.”
TreeFam: 2008 Update (2007, background): “In addition to the databases mentioned above, many other databases provide animal gene families on the genome-wide scale, such as PANTHER (9), Phylofacts (10), PhIGs (11) and SYSTERS (12).”
A human functional protein interaction network and its application to cancer data analysis (2010, methodology): “…for predicted FIs(cid:2) Reactome [23] Panther [60] KEGG [63] TRED [64] NCI-BioCarta [62] NCI-Nature [62] CellMap [61] Reactome [23] Panther [60] KEGG [63] TRED [64] NCI-BioCarta [62] NCI-Nature [62] CellMap [61] Na gans ) orthologs of the two human proteins; 4, whether there is a reported…”
Ortholog identification in the presence of domain architecture rearrangement (2011, methodology): “A related approach was developed for the functional annotation of the human genome [22], using the SCI-PHY algorithm [23] to identify functional subfamilies, and subsequently extended into two phylogenomic databases of gene family phylogenies: the PANTHER tools [24] and the PhyloFacts resource [25, ”
Phytozome: a comparative platform for green plant genomics (2011, methodology): “Protein-coding genes from both JGI and non-JGI genomes are then assigned PFAM domains (26), KEGG enzyme classification and KEGG Orthology assignment (27), KOG assignment (28) and Panther classification (29).”
Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets (2010, methodology): “For that purpose, we obtained a list of genes and their corresponding families and sub-families from the PANTHER database [27].”
InterPro: the integrative protein signature database (2008, methodology): “Since then, six other member databases have also joined and their data has been integrated: SMART (6), TIGRFAMs (7), PIRSF (8), SUPERFAMILY (9), PANTHER (10) and Gene3D (11).”
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis (2009, methodology): “Moreover, single proteomes were downloaded from GiardiaDB (18), Panther (19), Rice Genome Annotation Project (20), Dictybase (21), CGD (22), University of Tokyo (Cyanidioschyzon merolae Genome Project: http://merolae.”
V600EBRAF is associated with disabled feedback inhibition of RAF–MEK signaling and elevated transcriptional output of the pathway (2009, background): “The remaining 36 genes in the profile have not been previously identified as components of ERK signaling networks in published databases (23, 24).”
PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools (2009, methodology): “PANTHER Pathway is one of the modules within PANTHER (Mi et al. 2007).”
The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species (2009, methodology): “The P-POD [15] and PANTHER [16,17] databases are already using these sets, with PANTHER computing phylogenetic trees and P-POD providing results from both the OrthoMCL [18] and InParanoid [19] algorithms.”
An extended transcriptional network for pluripotency of embryonic stem cells. (2008, methodology): “Functional classification of the presumptive targets of each factor using the PANTHER classification tool also demonstrates separation of factors in two classes (Mi et al., 2007).”
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium (2009, methodology): “We then used this initial model as input, in addition to the sequences themselves, to the buildmodel program using the same parameters as in (7).”