Medical Physics Research Today is a free monthly online journal that collates and summarizes the latest research about Medical Physics, including details on medicine, radiotherapy, biomechanics, medical imaging.

Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks.

Colecchia F, Kottwitz D, Wagner M, Pfenninger CV, Thiel G, Tamm I, Peterson C, Nuber UA

Lund Strategic Research Center for Stem Cell Biology, Lund University, Computational Biology and Biological Physics, Lund University, Sweden, Department of Hematology and Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow, Berlin, Germany, University of Saarland Medical Center, Homburg, Germany and Department of Oncology, University Hospital, Lund, Sweden.

The prediction of transcription factor binding sites in genomic sequences is in principle very useful to identify upstream regulatory factors. However, when applying this concept to genomes of multicellular organisms such as mammals, one has to deal with a large number of false positive predictions since many transcription factor genes are only expressed in specific tissues or cell types. We developed TS-REX, a database/software system that supports the analysis of tissue and cell type-specific transcription factor-gene networks based on expressed sequence tag abundance of transcription factor-encoding genes in UniGene EST libraries. The use of expression levels of transcription factor-encoding genes according to hierarchical anatomical classifications covering different tissues and cell types makes it possible to filter out irrelevant binding site predictions and to identify candidates of potential functional importance for further experimental testing. TS-REX covers ESTs from H. sapiens and M. musculus, and allows the characterization of both presence and specificity of transcription factors in user-specified tissues or cell types. The software allows users to interactively visualize transcription factor-gene networks, as well as to export data for further processing. TS-REX was applied to predict regulators of Polycomb group genes in six human tumor tissues and in human embryonic stem cells.

Published 23 June 2009 in Nucleic Acids Res, 37(11): e82.
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Articles on Medical Physics published 22 June 2009:

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