PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

@article{Mi2018PANTHERV1,
  title={PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools},
  author={Huaiyu Mi and Anushya Muruganujan and Dustin Ebert and Xiaosong Huang and Paul D. Thomas},
  journal={Nucleic Acids Research},
  year={2018},
  volume={47},
  pages={D419 - D426}
}
Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life. We report the improvements we have made to the resource during the past two years. For evolutionary classifications, we have added more prokaryotic and plant genomes to the phylogenetic gene trees, expanding the representation of gene evolution in these lineages. We have refined many protein… 

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References

SHOWING 1-10 OF 22 REFERENCES

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

The current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data are described, which include stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.

PANTHER version 10: expanded protein families and functions, and analysis tools

The latest version of PANTHER, 10.0, includes almost 5000 new protein families (for a total of over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 104 fully sequenced genomes spanning all kingdoms of life.

Large-scale gene function analysis with the PANTHER classification system

This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system, and redesigned the website interface to improve both user experience and the system's analytical capability.

TreeFam v9: a new website, more species and orthology-on-the-fly

An HMM-based sequence search that places a user-provided protein sequence into a TreeFam gene tree and provides quick orthology prediction and a new approach to visualize gene trees and alternative displays that focuses on showing homology information from a species tree point of view are presented.

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

This article describes how PAINT is used to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines.

PANTHER: a library of protein families and subfamilies indexed by function.

The PANTHER/X ontology is used to give a high-level representation of gene function across the human and mouse genomes, and the family HMMs are used to rank missense single nucleotide polymorphisms (SNPs) according to their likelihood of affecting protein function.

Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

Three web services are implemented that address the need for information about evolutionarily related proteins to assess the likelihood of a deleterious effect on protein function arising from a single substitution at a specific amino acid position in the protein.

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

Insight is given into the origins and evolution of peptidase families, including an expansion in the number of proteasome components in Asgard archaeotes and as organisms increase in complexity.

PANTHER pathway: an ontology-based pathway database coupled with data analysis tools.

  • H. MiP. Thomas
  • Biology, Computer Science
    Methods in molecular biology
  • 2009
This chapter first discusses how biological knowledge is represented, particularly the importance of ontologies or standards in systems biology research, and uses PANTHER Pathway as an example to illustrate how ontologies and standards play a role in data modeling, data entry, and data display.

UniProt: the Universal Protein knowledgebase

The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.