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ToppGene

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A one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis. A P-value of each annotation of a test gene is derived by random sampling of the whole genome. The protein-protein interaction network (PPIN)-based disease candidate gene prioritization uses social and Web networks analysis algorithms (extended versions of the PageRank and HITS algorithms, and the K-Step Markov method).

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.

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.

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.