Advantages of Biobase's TRANSFAC over and above what is freely available?

Question

[vlaufer]

First, I have contacted Biobase about this but wanted an independent opinion.

At this URL, 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:

Available information:

• 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).

Unique service:

• 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

Answer 1

[Alex Reynolds]

As to whether TRANSFAC is useful to you will likely depend on what you would use it for. Our lab has used TRANSFAC in conjunction with other published databases like JASPAR and UniPROBE for statistical comparison with de novo discovered motifs, so as to determine if a discovered motif closely resembles a published model, or if it is something that is perhaps novel. I have used its classification table to map models to protein superclass, class, family and subfamilies, to see if there were interesting patterns in sets of TFs.

I don't recall ever using GUI tools - just parsing the text files in the bundle for the needed data. Those tools might be useful to you, depending on what you're trying to do.

This paper suggests methods for measuring similarities between TF databases. Given updates to JASPAR and TRANSFAC since publication, I don't know how useful the results would be. But it might be useful for clustering models from the publicly available TF databases, at least, just to see how those shake out.

Answer 2

[nta]

Genexplain recently uploaded a white paper explaining the difference between TRANSFAC and JASPAR. It seems when we use TRANSFAC there are chances that we don't miss important matrices that play a role in regulation of gene of interest. The white paper link can be found here:

https://genexplain.com/wp-content/uploads/2023/01/TRANSFAC-revealed-IRF3-site-in-SNPs-associated-with-high-severity-of-Covid-19-missed-by-JASPAR.pdf