Services

PANTHER services have been designed to work independently as well as part of large workflows. The complete PANTHER OpenAPI Specification can be found here. Refer to the details page for more information.

PANTHER services combine utilities to make correlations on large data sets as well as access to extensive genome lists with annotations by expert curators. In addition to gene lists, services are available to access PANTHER's set of gene families. PANTHER services can be grouped into three categories:

 Utilities

• Overrepresentation test: This test tool, compares a test gene list to a reference gene list, and determines whether a particular class (e.g. molecular function, biological process, cellular component, PANTHER protein class, the PANTHER pathway or Reactome pathway) of genes is overrepresented or underrepresented.
• Statistical enrichment: For each term in the specified annotation data set, the genes associated with that term are evaluated according to the likelihood that their numerical values were drawn randomly from the overall distribution of values.
• Ortholog service: Returns list of orthologs for a given set of genes
• Homolog service: Given a gene and an amino acid position, returns list of homologs for the gene and corresponding amino acid positions

 Data Mapping

• Mapping: Given a list of genes and a species, this service will return the list of genes that are mapped in PANTHER and also return any gene ontology annotations, PANTHER protein class annotations and Reactome annotations.

 PANTHER Phylogenetic Tree services

Genes from a single species by themselves may seem to be orthogonal, however, PANTHER has combined them into groups based on Hidden Markov Models and created families of phylogenetic trees using the tree of life. The trees have been annotated with Gene Ontology terms, PANTHER Protein Class terms, Panther Pathway Components and also Reactome pathways by expert curators. The phylogenetic trees leverage the evolutionary history and relationships amongst the species to group related genes from various taxonomies. Furthermore, evolutionary biologists have annotated genes within the trees using the principles of evolutionary inference as described in Gaudet et al, Briefings in Bioinformatics, 2011. The PANTHER® Evolutionary Species Tree Explorer can be utilized to condense the taxonomic domain and generate customized lists of gene families and supported taxonomies. The family identifiers and taxonomies can be used to focus on areas of specialization. The following services are available:

• Tree service: Returns the tree topology for the family in addition to annotation information. The optional taxonomic filter parameter can be utilized to prune out sequences not belonging to the specified set.
• MSA service: Returns the Multiple Sequence Alignment Information for a given PANTHER family. The optional taxonomic filter parameter can be utilized to prune out sequences not belonging to the specified set.
• Family ortholog: For a given family and set of taxonomies, returns all ortholog genes for the specified taxonomies.