TRANSFAC: an integrated system for gene expression regulation

By E. Wingender, Xin Chen, R. Hehl, H. Karas, I. Liebich, V. Matys, T. Meinhardt, M. Prüß, I. Reuter, F. Schacherer. Nucleic Acids Res., 2000

1,296 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/756aae95b3ccc3d5e5a8fd8d319b0f9501db6e91

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Citations in the corpus

Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. (2002, methodology): “Both the programs use weight matrix-based models (Stormo 2000) to represent ungapped DNA sequence motifs.”
A global map of p53 transcription-factor binding sites in the human genome. (2006, methodology): “, 2002) and the p53PET model with its weight matrix replaced by the one in the TRANSFAC database (Wingender et al., 2000).”
What is Bioinformatics? A Proposed Definition and Overview of the Field (2001, background): “Such classifications are provided in the secondary sequence databases described earlier and also those that specialise in regulatory proteins such as RegulonDB [73] and TRANSFAC [74].”
Detection of functional DNA motifs via statistical over-representation. (2004, methodology): “Two such libraries are used here: Jaspar (16), with 108 motifs, and the 428 vertebrate motifs from the Transfac Professional database version 6.3 ( 17 ).”
The rainbow trout (Oncorhynchus mykiss) Mx1 promoter (2001, methodology): “The TRANSFAC database [44] was used to search for binding sites of known transcription factors.”
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences (2002, methodology): “These queries result in a listing of entries with links to other information within the database or beyond through accession numbers from other databases, such as EMBL, GenBank, TRANSFAC (4) and MEDLINE.”
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. (2003, background): “Evolutionary conservation of regulatory elements in vertebrate hox gene clusters Simona Santini, Jeffrey L. Boore and Axel Meyer Genome Research (2003) Vol. 13, pp. 1111–1122 The conservative nature of natural selection renders functionally important genomic sequences far more resistant to change…”
Cluster-Buster: finding dense clusters of motifs in DNA sequences (2003, background): “A limited number of built-in motifs are provided as checkboxes and matrices can be copied and pasted directly from the TRANSFAC website (16).”
A new approach to decoding life: systems biology. (2001, methodology): “For instance, the Database of Interacting Proteins (137), BIND (10), and MIPS (90a) contain searchable indices of known protein-protein interactions; TRANSFAC (133) and SCPD (142) catalog interactions between proteins and DNA (i.e., transcriptionfactor interactions), and databases of metabolic pathw”
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors (2003, neutral): “jp/htdocs/PLACE], TRANSFAC [[12]http://transfac.”
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).”
Quantifying similarity between motifs (2007, positive): “The figure shows a set of PDFs for a particular query motif of length 12, computed relative to the TRANSFAC database.”