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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, Federico LU ; Kottwitz, Denise LU ; Wagner, Mandy; Pfenninger, Cosima LU ; Thiel, Gerald; Tamm, Ingo; Peterson, Carsten LU and Nuber, Ulrike LU (2009) In Nucleic Acids Research 37(11). p.82-82
Abstract
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nucleic Acids Research
volume
37
issue
11
pages
82 - 82
publisher
Oxford University Press
external identifiers
  • wos:000267441800005
  • pmid:19443447
  • scopus:67649890653
ISSN
1362-4962
DOI
10.1093/nar/gkp311
language
English
LU publication?
yes
id
e7d56b83-d336-434d-b596-2fdf5e543c26 (old id 1412260)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/19443447?dopt=Abstract
date added to LUP
2009-06-03 12:56:57
date last changed
2017-01-01 07:29:58
@article{e7d56b83-d336-434d-b596-2fdf5e543c26,
  abstract     = {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.},
  author       = {Colecchia, Federico and Kottwitz, Denise and Wagner, Mandy and Pfenninger, Cosima and Thiel, Gerald and Tamm, Ingo and Peterson, Carsten and Nuber, Ulrike},
  issn         = {1362-4962},
  language     = {eng},
  number       = {11},
  pages        = {82--82},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {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.},
  url          = {http://dx.doi.org/10.1093/nar/gkp311},
  volume       = {37},
  year         = {2009},
}