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Genie: literature-based gene prioritization at multi genomic scale

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Item Type:Article
Title:Genie: literature-based gene prioritization at multi genomic scale
Creators Name:Fontaine, J.F. and Priller, F. and Barbosa-Silva, A. and Andrade-Navarro, M.A.
Abstract:Biomedical literature is traditionally used as a way to inform scientists of the relevance of genes in relation to a research topic. However many genes, especially from poorly studied organisms, are not discussed in the literature. Moreover, a manual and comprehensive summarization of the literature attached to the genes of an organism is in general impossible due to the high number of genes and abstracts involved. We introduce the novel Genie algorithm that overcomes these problems by evaluating the literature attached to all genes in a genome and to their orthologs according to a selected topic. Genie showed high precision (up to 100%) and the best performance in comparison to other algorithms in most of the benchmarks, especially when high sensitivity was required. Moreover, the prioritization of zebrafish genes involved in heart development, using human and mouse orthologs, showed high enrichment in differentially expressed genes from microarray experiments. The Génie web server supports hundreds of species, millions of genes and offers novel functionalities. Common run times below a minute, even when analyzing the human genome with hundreds of thousands of literature records, allows the use of Genie in routine lab work. Availability: http://cbdm.mdc-berlin.de/tools/genie/.
Keywords:Animal Models, Algorithms, Gene Expression Profiling, Genes, Genomics, Heart, Internet, Medline, Software, Animals, Mice, Zebrafish
Source:Nucleic Acids Research
Publisher:Oxford University Press
Number:Suppl 2
Page Range:W455-W461
Date:July 2011
Official Publication:https://doi.org/10.1093/nar/gkr246
PubMed:View item in PubMed

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