First, I have contacted Biobase about this but wanted an independent opinion.
At this URL: www.biobase-international.com/product/transcription-factor-binding-sites Biobase describes a service called TRANSFAC TFBS. I am trying to determine whether or not it is worth paying for by determining how much of this information is I could get from other sources versus how much is available from other sources.
For example, what makes the track for Schema for TFBS Conserved - HMR Conserved Transcription Factor Binding Sites at http://genome.ucsc.edu/cgi-bin/hgTables on the UCSC website, different from what they offer?
Is the difference their GUI, or is it the actual information that can be accessed different?
Can anyone remark on the differences between the services Biobase names, below, from publicly available information? Or what databases they are drawn from?
To me, it seems like the following:
- 38,000+ transcription factor binding site reports containing details from the primary literature for more than 300 species, with a focus on human, mouse, rat, yeast, and plants
- 17,000+ miRNA target sites and 900+ miRNA reports
- 21,000+ transcription factor reports, a subset of which provide GO functional assignments, disease associations and expression pattern assignments
- 13,843,000+ ChIP fragment reports, many with best scoring site prediction for the respective factor, sequences (FASTA) and lists of adjacent genes are downloadable by ChIP Experiment
- 297,000+ promoter reports including mapped TF-binding sites, ChIP-chip/Seq based TF-binding fragments, histone modification locations, transcription start sites, and single nucleotide polymorphisms (SNPs)
These appear to me all to correspond to publicly available databases (if anyone can confirm this independent confirmation would help set my mind at ease).
- Interlinked reports connecting transcription factors, their experimentally-characterized binding sites and regulated genes, and associated ChIP fragments
- The Match™ tool for predicting transcription factor binding sites based on 5,000+ positional weight matrices (PWMs) derived from experimentally verified data and 3D homology modeling
- A tool for matrix comparison
- A pathway visualization tool for building custom regulatory networks out of experimentally demonstrated factor-DNA and factor-factor interactions
Thank you very much