Genie: literature-based gene prioritization at multi genomic scale
| Autor: | Jean-Fred Fontaine, Florian Priller, Miguel A. Andrade-Navarro, Adriano Barbosa-Silva |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
Web server
Biotechnologie [F06] [Sciences du vivant] MEDLINE Genomics Computational biology Biology computer.software_genre Genome Mice Genetics Animals Humans Biotechnology [F06] [Life sciences] Gene Organism Zebrafish Internet Gene Expression Profiling Heart Zebrafish/embryology/genetics Articles Automatic summarization Gene expression profiling Genes Models Animal Human genome computer Algorithms Heart/embryology Software |
| Zdroj: | Nucleic acids research, 39(Web Server issue), 455-61. England (2011). Nucleic Acids Research |
| Popis: | 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 eval- uating 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 en- richment in differentially expressed genes from microarray experiments. The Genie web server sup- ports 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/. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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