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URL: http://fgp.huck.psu.edu/tribedb/index.pl

Proper Citation: PlantTribes (RRID:SCR_007863)

Description: It is an objective classification system for plan proteins based on cluster analyses of the inferred proteomes of the sequenced angiospermsArabidopsis thaliana v Columbia, Oryza sativa v. japonica (Rice), and Populus trichocarpa (poplar). Sequence data for Carica papaya and Medicago papaya are also included in the current version of Tribes. Results for these species are currently masked from view, but will be available when the genomes are publicly released. In addition to the genome-based tribe scaffold, unigenes from more than 200 plant and algal species TIGR Transcript Assemblies have been associated with each tribe (see documentation), resulting in a global classification of about 4 million putative plant protein sequences. PlantTribes 1.0 incorporates an extensive collection of microarray expression data from Arabidopsis microarray experiments. Expression data is linked to the individual genes in PlantTribes, and can be accessed through any result including Arabidopsis gene sequences. PlantTribes is based on the similarity-based clustering procedure TribeMCL (Enright et al, 2002,2003) to classify protein-coding genes into putative gene families. MCL classifications have been constructed using three clustering stringencies , allowing the user to explore the stability of the protein classification. A second round of MCL clustering identifies SuperTribes that approximate objective superfamilies. PlantTribes also includes information about domains, traditional gene family names, and a unified nomenclature based on common terms.

Synonyms: PlantTribes

Resource Type: data or information resource, database