Reference : Genie: literature-based gene prioritization at multi genomic scale.
Scientific journals : Article
Life sciences : Biotechnology
Systems Biomedicine
http://hdl.handle.net/10993/26646
Genie: literature-based gene prioritization at multi genomic scale.
English
Fontaine, Jean-Fred [> >]
Priller, Florian [> >]
Barbosa Da Silva, Adriano mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Andrade-Navarro, Miguel A. [> >]
2011
Nucleic acids research
39
Web Server issue
W455-61
Yes (verified by ORBilu)
International
0305-1048
1362-4962
England
[en] Algorithms ; Animals ; Gene Expression Profiling ; Genes ; Genomics ; Heart/embryology ; Humans ; Internet ; MEDLINE ; Mice ; Models, Animal ; Software ; Zebrafish/embryology/genetics
[en] 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 Genie 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/.
http://hdl.handle.net/10993/26646

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Open access
genie.pdfPublisher postprint2.84 MBView/Open

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.