PANTHER
| Content | |
|---|---|
| Description | The PANTHER database classifies gene products into families |
| Data types captured |
Gene families |
| Contact | |
| Research center | University of Southern California |
| Authors | Paul D Thomas |
| Primary citation | PMID 12520017 |
| Access | |
| Website | [1] |
| Miscellaneous | |
| Bookmarkable entities |
yes |
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. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput analysis.
The project consists of both manual curation and bioinformatics algorithms. Proteins are classified according to family (and subfamily), molecular function, biological process and pathway. It is one of the databases feeding into the European Bioinformatics Institute's InterPro database.—Application of PANTHER—The most important application of PANTHER is to accurately infer the function of uncharacterized genes from any organism based on their evolutionary relationships to genes with known functions. 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. Shortly, using the data and tools on the PANTHER, users will be able to:
In panther there is a pythogenetic tree for each of the protein families. The annotation of tree is done based on the following criteria:
To generate phylogenetic trees, PANTHER uses GIGA algorithm. GIGA uses species tree to develop tree construction. 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. This data is then used as an input for GIGA program. The output tree from GIGA are labelled. Each internal node is labelled as whether divergence event happened as speciation or gene duplication.
...
Wikipedia