Database TRANSFAC

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

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. 

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

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. 

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). 

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). 

TransFac contains substantially more PWMs than the Jaspar database. However, many PWMs are redundant and represent the same TF. For test runs, it is recommended to only select the Jaspar database to speed up computation. 

To view information from TransFac database, a registration may be required, which is free for academic users. Information about most recent additions to the database is available only to commercial users. Entries, for which information is not publicly available, are marked Pro only and linked to TransFac Pro database. 

Prokaryotic and eukaryotic RNA transcriptions show strong parallels though there are several important differences. A major distinction between prokaryotes and eukaryotes is the move from one prokaryotic enzyme that can faithfully transcribe DNA into RNA to three eukaryotic RNA polymerases. The eukaryotic RNA transcripts are precursors (e.g. pre-mRNA, pre-rRNA and pre-tRNA), which undergo processing to form respective mature RNAs. Furthermore, eukaryotic mRNAs are polyadenylated. A database for mammalian mRNA polyadenylation is available at PolyA DB (http // polya.umdnj.edu/polyadb). The eukaryotic transcription is tightly regulated and various proteins/factors known as transcription factors (TF) are involved in the eukaryotic transcription. The classification of transcription factors can be found at TRANFAC (http //transfac.gbf.de/TRANFAC/cl/cl.html). 

Matys, V., O. V. Kel-Margouhs, et al. (2006). "TRANSFAC and its module TRANSComjjel transcriptional gene regulation in eukaryotes." Nucleic Adds Res(34 Database) D108-110. 

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