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          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents



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ID: 536318.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
Targetfinder.org: a resource for systematic discovery of transcription factor target genes
Authors:Kielbasa, S. M.; Bluthgen, N.; Fahling, M.; Mrowka, R.
Language:English
Date of Publication (YYYY-MM-DD):2010-07-01
Title of Journal:Nucleic Acids Research
Journal Abbrev.:Nucleic Acids Res
Volume:38 Suppl
Start Page:W233
End Page:W238
Copyright:© 2010 Oxford University Press
Review Status:not specified
Audience:Experts Only
Abstract / Description:Targetfinder.org (http://targetfinder.org/) provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13,000 genes). The primary application of Targetfinder.org is to expand a list of known transcription factor targets by new candidate target genes. The user submits a group of genes (the 'seed'), and as a result the web site provides a list of other genes ranked by similarity of their expression to the expression of the seed genes. Additionally, the web site provides information on a recovery/cross-validation test to check for consistency of the provided seed and the quality of the ranking. Furthermore, the web site allows to analyse affinities of a selected transcription factor to the promoter regions of the top-ranked genes in order to select the best new candidate target genes for further experimental analysis.
Free Keywords:Gene Expression Profiling; Gene Expression Regulation; Internet; Oligonucleotide Array Sequence Analysis; Promoter Regions, Genetic; Software; Transcription Factors/metabolism
External Publication Status:published
Document Type:Article
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
External Affiliations:Institute of Pathology, Institute of Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1 and Institute of Physiology, AG Systems Biology, Charité Universitätsmedizin Berlin, Tucholskystr. 2, D-10117 Berlin, Germany
Identifiers:ISSN:1362-4962 (Electronic) 0305-1048 (Linking) %R gkq3... [ID No:1]
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=... [ID No:2]
DOI:10.1093/nar/gkq374 [ID No:3]
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