PANTHER Classification System

Category Cross-Omics>Pathway Analysis/Tools

Abstract The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into 'families and subfamilies' [see (A) below] of shared function, which are then categorized by molecular function and biological process 'ontology terms' [see (B) below]. For an increasing number of proteins, detailed biochemical interactions in canonical pathways [see (C) below] are captured and can be viewed interactively.

The PANTHER Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. Proteins have been classified according to:

1) Family and subfamily: families are groups of evolutionarily related proteins; subfamilies are related proteins that also have the same function.

2) Molecular function: the function of the protein by itself or with directly interacting proteins at a biochemical level, e.g. a protein kinase.

3) Biological process: the function of the protein in the context of a larger network of proteins that interact to accomplish a process at the level of the cell or organism, e.g. mitosis.

4) Pathway: similar to biological process, but a pathway also explicitly specifies the relationships between the interacting molecules.

Note: The PANTHER Classifications are the result of human curation as well as sophisticated bioinformatics algorithms.

A) Families and Subfamilies:

Families and hidden Markov models (HMMs) - PANTHER version 6.1 contains 5,547 protein families, divided into 24,582 functionally distinct protein subfamilies by expert biologist curators. Each protein family is represented by a phylogenetic tree defining its subfamilies. Families and subfamilies are also represented by HMMs and associated with functional ontology terms. For PANTHER version 6.1, the UniProt protein database was clustered using a basic local alignment search tool (BLAST)-based similarity score, and the resulting dendrogram was used to define the protein families.

B) Ontology Terms:

Ontologies - The PANTHER/X ontology is a controlled vocabulary of molecular function and biological process terms, arranged as directed acyclic graphs (DAGs) similar to the Gene Ontology (GO), but greatly abbreviated and simplified to facilitate high-throughput analyses.

C) Pathways:

PANTHER Pathway consists of over 139, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. A component is usually a single protein in a given organism, but multiple proteins can sometimes play the same role. Pathways are drawn using 'CellDesigner software' [see (D) below] , capturing molecular level events in both signaling and metabolic pathways, and can be exported in systems biology markup language (SBML) format. Pathway diagrams are interactive and include tools for visualizing 'gene expression data' [see (E) below] in the context of the diagrams.

D) CellDesigner software -

CellDesigner is a modeling tool of biochemical networks with a graphical user interface. It is designed to be systems biology workbench (SBW) compliant and support the systems biology markup language (SBML) format.

E) Gene Expression Data analysis:

PANTHER expression analysis tools can be used for microarray data intrepretation. Multiple gene lists can be mapped to PANTHER molecular function and biological process categories, as well as to biological pathways. PANTHER pathway visualization tool will display your experimental results on detailed diagrams of the relationships between genes/proteins in known pathways.

System Requirements

PC Users (Recommended):

Macintosh Users:

For both:

Browse the PANTHER system using the Prowler, and retrieve results for different data associated with the ontology and pathway terms, such as individual genes or families and subfamilies of proteins. About the PANTHER Ontologies

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