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# Pythologentic Tree Building
# Pythologentic Tree Building
# Annotation of Tree Nodes
# Annotation of Tree Nodes

=== Family Clustering ===
===== Sequence Set: ===== PANTHER trees depicts gene family evolution from broad selection of fully sequences genes. PANTHER have one sequence per gene so that tree can represent event occurred over the course of evolution i.e duplication, speciation.
PANTHER genomes set are selected based on following criteria.
The set should include major experimatal model organism, this will assit in depicting functional information of the organism which are less studied.
The set should include broad taxonomic range of other genomes, prederably fully sequenced and annoted this will help relating experimental model organism.

===== Family Clusters: ===== Following are the requirements for family clusters

#The family must contain atleast five total memebers and one member atleast from a Genetic Ontology (GO) reference genome
#The data should have sequence alignment of good qulity so it can support pythologenetic event
#The assessment of multiple aligened sequence is done by assessing length of the aligned sequence, atleast 30 sites aligned across 75% or more of family member
=== Phylogenetic Tree Building ===
For each family multiple sequence are aligned using default setting of MAFFT, any column which 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 internalnode labelled as whether divergence event happened as speciation or gene duplication.

=== Annotation of tree nodes ===
Each node in PANTHER tree is annotated with heritable attribute. Herritable attribute can be of three types subfamily membership, gene function and protein class membership. These annotation of nodes applies to primary sequence which was used to construct tree. In applying these annotation to primariy sequence simple evolutionary principle is used ie. Each node annotation Is propagated by its decendece node




Revision as of 07:38, 9 September 2014

For other uses, see Panther (disambiguation).
PANTHER
Content
DescriptionThe PANTHER database classifies gene products into families
Data types
captured		Gene families
Contact
Research centerUniversity of Southern California
AuthorsPaul D Thomas
Primary citationPMID 12520017
Access
Website[1]
Miscellaneous
Bookmarkable
entities		yes

In bioinformatics the PANTHER (Protein ANalysis THrough Evolutionary Relationships) classification system is a biological database that can be used to classify and identify the function of gene products.[1] PANTHER is part of the Gene Ontology Reference Genome Project[2] designed to classify proteins and their genes for high-throughput analysis.

The project consists of both manual curation and bioinformatics algorithms.[3] 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.[4]


PANTHER

Protein Analysis Through Evolutuonary Relationship (PANTHER) is a database aim to delivery high-throughput analysis of proteins sequences. One of the interesting feature of this PANTHER is that user can browse the database based on protein function. Another interesting feature of PANTHER db it draws protein sequence in pythalogic tree format for each sub-family.

PANTHER History

  • 1998:Project was launched at Molecular Application Group.
  • 1999:Acquired by Celera Genomics.
  • 2000:PANTHER 1 released in Celera Discovery Systems (CDS).
  • 2001: PANTHER 2 released, which is used in the annotationon of the first published human genome Celera.
  • 2002: PANTHER 3 released. PANTHER annotations are integrated in FlyBase.Moved to ABI
  • 2003: PANTHER 4 released with the public release of PANTHER Classification System.
  • 2005: PANTHER 5 released with PANTHER Pathway and analysis tool.Establish collabora3on with Interpro.
  • 2006: PANTHER 6 released. Move to SRI.
  • 2010: PANTHER 7 released.
  • 2011: Move to USC.
  • 2012: PANTHER 8 released.
  • 2014: PANTHER 9 released

Phylogenetic Tree

In panther there is a pythogenetic tree for each of the protein families. Each of the node in this tree is annotated gene attributes. This gene attribute depicts ‘subfamily membership’, ‘protein class’ and gene function. Intersting part of this tree functionality is that internal node also depicts evolutionary event i.e speciation, gene duplication, horizontal gene transfer. In addition to this tree are annoted with gene ontology(GO) terms. Gene ontology is part of reference genome project. To generate pythologic tree PANTHER uses GIGA algorithm. GIGA uses species tree to develop tree construction on every iterationit attemp to reconcile tree in event form of speciation, gene duplication

PANTHER Library Data Generation Process

The process for data generation is divided in three step

  1. Family Clustering
  2. Pythologentic Tree Building
  3. Annotation of Tree Nodes

Family Clustering

===== Sequence Set: ===== PANTHER trees depicts gene family evolution from broad selection of fully sequences genes. PANTHER have one sequence per gene so that tree can represent event occurred over the course of evolution i.e duplication, speciation. PANTHER genomes set are selected based on following criteria. The set should include major experimatal model organism, this will assit in depicting functional information of the organism which are less studied. The set should include broad taxonomic range of other genomes, prederably fully sequenced and annoted this will help relating experimental model organism.

===== Family Clusters: ===== Following are the requirements for family clusters

  1. The family must contain atleast five total memebers and one member atleast from a Genetic Ontology (GO) reference genome
  2. The data should have sequence alignment of good qulity so it can support pythologenetic event
  3. The assessment of multiple aligened sequence is done by assessing length of the aligned sequence, atleast 30 sites aligned across 75% or more of family member

Phylogenetic Tree Building

For each family multiple sequence are aligned using default setting of MAFFT, any column which 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 internalnode labelled as whether divergence event happened as speciation or gene duplication.

Annotation of tree nodes

Each node in PANTHER tree is annotated with heritable attribute. Herritable attribute can be of three types subfamily membership, gene function and protein class membership. These annotation of nodes applies to primary sequence which was used to construct tree. In applying these annotation to primariy sequence simple evolutionary principle is used ie. Each node annotation Is propagated by its decendece node





External References

Description of PANTHER

References

  1. ^ Thomas, PD.; Kejariwal, A.; Campbell, MJ.; Mi, H.; Diemer, K.; Guo, N.; Ladunga, I.; Ulitsky-Lazareva, B.; et al. (Jan 2003). "PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification". Nucleic Acids Res. 31 (1): 334–41. doi:10.1093/nar/gkg115. PMC 165562. PMID 12520017.
  2. ^ GO Reference Genome Annotation Project
  3. ^ Mi, H.; Muruganujan, A.; Thomas, PD. (Jan 2013). "PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees". Nucleic Acids Res. 41 (Database issue): D377–86. doi:10.1093/nar/gks1118. PMID 23193289.
  4. ^ Hunter, S.; Jones, P.; Mitchell, A.; Apweiler, R.; Attwood, TK.; Bateman, A.; Bernard, T.; Binns, D.; et al. (Jan 2012). "InterPro in 2011: new developments in the family and domain prediction database". Nucleic Acids Res. 40 (Database issue): D306–12. doi:10.1093/nar/gkr948. PMC 3245097. PMID 22096229.
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