Skip Navigation


Nucleic Acids Research Advance Access originally published online on May 13, 2009
Nucleic Acids Research 2009 37(11):e82; doi:10.1093/nar/gkp311
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4737K) Freely available
Right arrow Screen PDF (710K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/11/e82    most recent
gkp311v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Colecchia, F.
Right arrow Articles by Nuber, U. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Colecchia, F.
Right arrow Articles by Nuber, U. A.
Related Collections
Right arrow Protein-nucleic acid interaction
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2009, Vol. 37, No. 11 e82
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

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

Federico Colecchia1,2, Denise Kottwitz1, Mandy Wagner3, Cosima V. Pfenninger1, Gerald Thiel4, Ingo Tamm3, Carsten Peterson1,2 and Ulrike A. Nuber1,5,*

1Lund Strategic Research Center for Stem Cell Biology, Lund University, 2Computational Biology and Biological Physics, Lund University, Sweden, 3Department of Hematology and Oncology, Charité-Universitätsmedizin Berlin, Campus Virchow, Berlin, Germany, 4University of Saarland Medical Center, Homburg, Germany and 5Department of Oncology, University Hospital, Lund, Sweden

*To whom correspondence should be addressed: Tel: +46 46 2221563; Fax: +46 46 2223600; Email: ulrike.nuber{at}med.lu.se

Received January 12, 2009. Revised April 15, 2009. Accepted April 17, 2009.

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.

The authors wish it to be known that, in their opinion, the second and third authors should be regarded as joint Second Authors.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.