The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
E Wingender - Briefings in bioinformatics, 2008 - academic.oup.com
Since its beginning as a data collection more than 20 years ago, the TRANSFAC project
underwent an evolution to become the basis for a complex platform for the description and …
underwent an evolution to become the basis for a complex platform for the description and …
Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
T Heinemeyer, X Chen, H Karas, AE Kel… - Nucleic acids …, 1999 - academic.oup.com
TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-
binding profiles. In addition to being updated and extended by new features, it has been …
binding profiles. In addition to being updated and extended by new features, it has been …
Visualization, documentation, analysis, and communication of large-scale gene regulatory networks
WJR Longabaugh, EH Davidson, H Bolouri - Biochimica et Biophysica Acta …, 2009 - Elsevier
Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally
distributed. These characteristics impose challenging demands on software tools for …
distributed. These characteristics impose challenging demands on software tools for …
[PDF][PDF] Identifying gene regulatory networks from experimental data
As biology enters an era where the genomes of several organisms have been completely
sequenced, the next great challenge is determining gene regulatory networks. Every gene …
sequenced, the next great challenge is determining gene regulatory networks. Every gene …
TRANSFAC: an integrated system for gene expression regulation
E Wingender, X Chen, R Hehl, H Karas… - Nucleic acids …, 2000 - academic.oup.com
TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-
binding profiles (http://transfac. gbf. de/TRANSFAC/). Its content has been enhanced, in …
binding profiles (http://transfac. gbf. de/TRANSFAC/). Its content has been enhanced, in …
The TRANSFAC system on gene expression regulation
E Wingender, X Chen, E Fricke, R Geffers… - Nucleic acids …, 2001 - academic.oup.com
The TRANSFAC database on transcription factors and their DNA-binding sites and profiles
(http://www. gene-regulation. de/) has been quantitatively extended and supplemented by a …
(http://www. gene-regulation. de/) has been quantitatively extended and supplemented by a …
Gene networks: how to put the function in genomics
P Brazhnik, A De La Fuente, P Mendes - TRENDS in Biotechnology, 2002 - cell.com
An increasingly popular model of regulation is to represent networks of genes as if they
directly affect each other. Although such gene networks are phenomenological because …
directly affect each other. Although such gene networks are phenomenological because …
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
We present the second and improved release of the TOUCAN workbench for cis-regulatory
sequence analysis. TOUCAN implements and integrates fast state-of-the-art methods and …
sequence analysis. TOUCAN implements and integrates fast state-of-the-art methods and …
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation
E Wingender, AE Kel, OV Kel, H Karas… - Nucleic Acids …, 1997 - academic.oup.com
Three databases that provide data on transcriptional regulation are described. TRANSFAC
is a database on transcription factors and their DNA binding sites. TRRD (Transcription …
is a database on transcription factors and their DNA binding sites. TRRD (Transcription …
[HTML][HTML] The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Background High-throughput genome biological experiments yield large and multifaceted
datasets that require flexible and user-friendly analysis tools to facilitate their interpretation …
datasets that require flexible and user-friendly analysis tools to facilitate their interpretation …