TRANSFAC

Wingender, E., Chen, X., Hehl, R., et al. (2000) TRANSFAC an integrated system for gene expression regulation. Nucleic Acids Res. 28, 316-319. 

METABOL ENERGY CCYC DNA TRSCRIPT PROTSYNT PROTFATE TRANSPRT DEFENSE ENIVRON CELLFATE CELL ORG SUBC LOG PROT ACT TRANSFAC NOTCLEAR UNCLASS... 

Various regulatory proteins are involved in the eukaryotic transcription (Johnson and McKnight, 1989). The classification of transcription factors can be found at TRANFAC (http //transfac.gbf.de/TRANFAC/cl/cl.html) (Wingender et al., 2001). 

Boehringer Mannheim EcoCyc KEGG, home KEGG Pathway site PathDB Soybase TRANSFAC American Type Culture Collection... 

TRANSFAC Database shtml all http //www.gene-regulation.com/cgi-bin/pub/... 

Proteomics ExPASy databases/transfac/search.cgi]. http //expasy.org/tools... 

Heinemeyer, T Chen, X., Karas, H., Kel, A. E., Kel, O. V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F. Wingender, E. (1999). Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res 27,318-22. 

This statistics has been implemented in the program NSITE (http // www.softberry.com/gf.html) [24], that identifies nonrandom similarity between fragments of a given sequence and consensuses of regulatory motifs from the TRANSFAC database [25]. 

Wingender E., Dietze P., Karas H., Knuppel R. (1996) TRANSFAC a database of transcription factors and their binding sites. Nucleic Acid. Res., 24, 238-241. 

MATRIX SEARCH http //bimas. dcrt.nih.gov/molbio/matrixs/ IMD matrix library (TRANSFAC + TFD)... 

TESS http //agave.humgen.upenn.edu/utess/tess/ TRANSFAC matrices... 

FunSiteP http //transfac.gbf.de/dbsearch/funsitep/fsp.html includes proximal promoter... 

There are several transcription factor databases. Transfac [32] and TFD [10] provide databases of transcription factors, their binding sites and the genes which regulate these transcriptions. 

Matys, V., Kel-Margoulis, O.V., Fricke, E., et al. (2006) TRANSFAC and its module TRANSCompel transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108-D110. 

Upon forwarding to the multiTF analysis initiation page, the user selects from methods and parameters to identify TFBS in individual sequences. First, the user has to choose between the use of the TRANSFAC database of TFBS (http //www.biobase.de/) or user-defined consensus sequences (Fig. 8A). 

Assuming the most common use of TRANSFAC PWM matrices in description of TFBS binding specificities to scan for binding sites, the user selects the appropriate library of phylogenies (including vertebrate, plant, fungi, nematodes, insects, and bacteria). 

The final option permits the selection of only high-specificity matrices in the TFBS annotation. This option subselects a list of TFBS matrices that have <= 0.85 cut-off similarity to the TRANSFAC PWM. These are the matrices with the most reliable definitions in the TRANSFAC database. 

The importance of motif discovery is born out by the growth in motif databases such as TRANSFAC, JASPAR, SCPD, DBTBS, RegulonDB (7-10) for DNA motifs and PROSITE, BLOCKS, and PRINTS (3-5) for protein motifs. However, far more motifs remain to be discovered. For example, TFBS motifs are known for only about 500 vertebrate TFs, but it is estimated that there are about 2000 TFs in mammalian genomes alone (7,11). 

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