The TRANSFAC system on gene expression regulation

By E. Wingender, Xin Chen, E. Fricke, R. Geffers, R. Hehl, I. Liebich, M. Krull, V. Matys, H. Michael, R. Ohnhäuser and 4 more. Nucleic Acids Res., 2001

714 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1b06cdf06bb350d75a191e7033c2306878d2fd99

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

MATCHTM: a tool for searching transcription factor binding sites in DNA sequences (2003, background): “Match uses a library of position weight matrices (PWMs) collected in the TRANSFAC(1) database (1) and therefore provides the possibility to search for a great variety of different transcription factor binding sites.”
BioAmbients: an abstraction for biological compartments (2004, methodology): “Pathway databases such as BIND [2] and TRANSPATH [23] incorporate some compartment hierarchy and localization information.”
From signatures to models: understanding cancer using microarrays (2005, background): “…overexpressed when Jun-B is underexpressed, consistent with reports suggesting that loss of Jun-B activity enabled epithelial mesenchymal transition in tumors 66 . promoter sequences, on the basis of experimentally determined sites 16 , de novo identification or evolutionary conservation 17,18 .”
TRANSFAC®: transcriptional regulation, from patterns to profiles (2003, background): “It is not only jointly used by several of our own databases, TRANSPATH1 (17), PathDB1 (8, 9 ), S/MARt DBTM (18), and TRANSCompel1 (19).”
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. (2004, methodology): “We also applied our regulog mapping method to yeast transcriptional regulation data sets (Wingender et al. 2001; Horak et al. 2002; Lee et al. 2002).”
PROMO: detection of known transcription regulatory elements using species-tailored searches (2002, background): “The TRANSFAC database (Wingender et al., 2001) contains the largest available collection of eukaryotic factorspecific weight matrices, which can be used to search for potential matches in a DNA sequence of interest, for example by the MatInspector program (Quandt et al., 1995).”
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections (2014, methodology): “A further limiting factor is that many methods are restricted to using human annotated PWMs (e.g. TRANSFAC [20], JASPAR [21] or UNIPROBE [22]), limiting the number of TFs that can be identified as candidate network regulators based on motif enrichment.”
GENOMIC DATA ANALYSIS (2004, methodology): “Some examples are the KEGG (Kanehisa and Goto, 2000) and LIGAND (Goto et al., 2000) databases, the STKE database (Gough, 2002), and the TRANSPATH (Krull et al., 2003) and TRANSFAC (Wingender et al., 2001) databases, which are used in paper V.”
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. (2002, background): “A thorough search of the Transfac database (Wingender et al. 2001; http://www.gene-regulation.de) and published literature indicated that the HSAS motif is novel and does not correspond to any known TF binding sites.”
Discovering regulatory and signalling circuits in molecular interaction networks (2002, positive): “To construct a large molecular interaction network for yeast, we included all 7145 protein–protein interactions in the BIND database (Bader et al., 2001) and all 317 protein→DNA interactions present in TRANSFAC (Wingender et al., 2001) as of September 2001.”
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics (2007, methodology): “Interaction data was gathered from a number of different published high-throughput datasets and published databases [2–5, 27, 34, 45, 46].”
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae (2005, background): “TRANSFAC is mostly focused on transcription factor-binding sites in higher eukaryotes and provides a limited number of binding sites for S.cerevisiae .”