Genie: literature-based gene prioritization at multi genomic scale
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Jean-Fred Fontaine
- Florian Priller
- Adriano Barbosa-Silva
- Miguel A Andrade-Navarro
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000292325300074&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1093/nar/gkr246
- eISSN
- 1362-4962
- Externe Identifier
- Clarivate Analytics Document Solution ID: 786RJ
- PubMed Identifier: 21609954
- ISSN
- 0305-1048
- Zeitschrift
- NUCLEIC ACIDS RESEARCH
- Paginierung
- W455 - W461
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Titel
- Genie: literature-based gene prioritization at multi genomic scale
- Sub types
- Article
- Ausgabe der Zeitschrift
- 39
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Jean-Fred Fontaine
- Florian Priller
- Adriano Barbosa-Silva
- Miguel A Andrade-Navarro
- DOI
- 10.1093/nar/gkr246
- eISSN
- 1362-4962
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- suppl_2
- Zeitschrift
- Nucleic Acids Research
- Sprache
- en
- Online publication date
- 2011
- Paginierung
- W455 - W461
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Herausgeber
- Oxford University Press (OUP)
- Herausgeber URL
- http://dx.doi.org/10.1093/nar/gkr246
- Datum der Datenerfassung
- 2018
- Titel
- Génie: literature-based gene prioritization at multi genomic scale
- Ausgabe der Zeitschrift
- 39
Datenquelle: Crossref
- Abstract
- <h4>Unlabelled</h4>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 Génie 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. Génie 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 Génie in routine lab work.<h4>Availability</h4>http://cbdm.mdc-berlin.de/tools/genie/.
- Addresses
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany. jean-fred.fontaine@mdc-berlin.de
- Autoren
- Jean-Fred Fontaine
- Florian Priller
- Adriano Barbosa-Silva
- Miguel A Andrade-Navarro
- DOI
- 10.1093/nar/gkr246
- eISSN
- 1362-4962
- Externe Identifier
- PubMed Identifier: 21609954
- PubMed Central ID: PMC3125729
- Open access
- true
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- Web Server issue
- Zeitschrift
- Nucleic acids research
- Schlüsselwörter
- Heart
- Animals
- Zebrafish
- Humans
- Mice
- Gene Expression Profiling
- Models, Animal
- Genomics
- Genes
- Algorithms
- Internet
- Software
- MEDLINE
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2011
- Open access status
- Open Access
- Paginierung
- W455 - W461
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Publisher licence
- CC BY-NC
- Datum der Datenerfassung
- 2011
- Titel
- Génie: literature-based gene prioritization at multi genomic scale.
- Sub types
- Research Support, Non-U.S. Gov't
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 39
Files
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21609954/pdf/?tool=EBI https://europepmc.org/articles/PMC3125729?pdf=render
Datenquelle: Europe PubMed Central
- Abstract
- UNLABELLED: 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 Génie 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. Génie 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 Génie in routine lab work. AVAILABILITY: http://cbdm.mdc-berlin.de/tools/genie/.
- Autoren
- Jean-Fred Fontaine
- Florian Priller
- Adriano Barbosa-Silva
- Miguel A Andrade-Navarro
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/21609954
- DOI
- 10.1093/nar/gkr246
- eISSN
- 1362-4962
- Externe Identifier
- PubMed Central ID: PMC3125729
- Ausgabe der Veröffentlichung
- Web Server issue
- Zeitschrift
- Nucleic Acids Res
- Schlüsselwörter
- Algorithms
- Animals
- Gene Expression Profiling
- Genes
- Genomics
- Heart
- Humans
- Internet
- MEDLINE
- Mice
- Models, Animal
- Software
- Zebrafish
- Sprache
- eng
- Country
- England
- Paginierung
- W455 - W461
- PII
- gkr246
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2011
- Titel
- Génie: literature-based gene prioritization at multi genomic scale.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 39
Datenquelle: PubMed
- Beziehungen:
- Eigentum von