In bioinformatics, the PANTHER (protein analysis through evolutionary relationships) classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products.
[3] Proteins are classified according to family (and subfamily), molecular function, biological process and pathway.
[3] By combining gene function, ontology, pathways and statistical analysis tools, PANTHER enables biologists to analyze large-scale, genome-wide data obtained from the current advance technology including: sequencing, proteomics or gene expression experiments.
On every iteration it attempts to reconcile tree in event form of speciation and gene duplication.
The process for data generation is divided into three steps: PANTHER trees depicts gene family evolution from a broad selection of genomes which are fully sequenced.
PANTHER have one sequence per gene so that the tree can represent event occurred over the course of evolution i.e duplication, speciation.
PANTHER genomes set are selected based on the following criteria: Following are the requirements for being family clusters in PANTHER: For each family multiple sequence are aligned using a default setting of MAFFT, any column which is aligned less than 75% of the sequence is removed.
Each internal node is labelled as whether divergence event happened as speciation or gene duplication.
Although PANTHER/X ontology has a hierarchical organization, it is a directed acyclic graph and so when it is biologically justified, child categories appear under more than one parent.
There are more support for alternative database identifiers for genes, proteins and microarray probes.
This stable identifier is a nine-digit number with the prefix PTN (stand for PANTHER Tree Node).
The home page of PANTHER website shows several folder tabs for major workflows, including: gene list analysis, browse, sequence search, cSNP scoring, and keyword search.
It gives you the information for all the three genes which are: Using this folder tab and by selecting the ontology you are interested in, you can browse different classification.
PANTHER will use an alignment of evolutionarily related proteins, calculate the substitution position-specific evolutionary conservation (subPSEC) and estimate the likelihood of this nonsynonymous coding SNP to lead a functional effect on the protein.