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PO / Plant Ontology
Produces structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information even as knowledge of the biology of the relevant plant taxa is accumulating and changing. Plant Ontology brings an integrated approach of adopting common annotation standards and a set of reference ontologies for Plants. The project is a heavily collaborative project that depends on coordination with several national and international projects.
ToppGene Suite
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Consists of a one-stop online assembly of computational software tools. ToppGene Suite enables users to (i) perform gene list enrichment analysis, (ii) perform candidate gene prioritization based on functional annotations, (iii) perform candidate gene prioritization based on protein interactions network analysis and (iv) identify and rank candidate genes in the interactome based on both functional annotations and e protein-protein interaction network (PPIN) analysis. The suite can identify true candidate genes.
DroPhEA / Drosophila Phenotype Enrichment Analysis
A core module of a web application that facilitates research in insect functional genomics through enrichment analysis on mutant phenotypes of fruit fly (Drosophila melanogaster). The phenotypes investigated in the analyses can be predefined by FlyBase or customized by users. DroPhEA allows users to specify mutation or ortholog types, displays enriched term results in a hierarchical structure and supports analyses on gene sets of all insect species with a fully sequenced genome.
modPhEA / MODel organism PHenotype Enrichment Analysis
Identifies enriched/depleted phenotypes of any one of six major model organisms: Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, Homo sapiens. modPhEA uses a predefined hierarchical structure, or as a phenotype catalog. It can provide novel and important biological insights. The tool allows users to analyze gene sets by limiting the phenotypic records derived from specific approaches in order to control for approach-specific biases.
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