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Journal Article

Targetfinder.org: a resource for systematic discovery of transcription factor target genes


Kielbasa,  S. M.
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

Mrowka,  R.
Max Planck Society;

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Kielbasa, S. M., Bluthgen, N., Fahling, M., & Mrowka, R. (2010). Targetfinder.org: a resource for systematic discovery of transcription factor target genes. Nucleic Acids Research, 38 Suppl, W233-W238. doi:10.1093/nar/gkq374.

Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-7ABB-B
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.