Coffee break with TRANSFAC

Welcome to the “Coffee break with TRANSFAC”

A series of online sessions hosted Dr. Alexander Kel, CEO geneXplain GmbH


The next Coffee break with TRANSFAC will be held on February 7th at 5 PM CET

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Second coffee break with TRANSFAC


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This initiative of Q&A sessions with a leading bioinformatics expert Dr. Alexander Kel is intended to support all researchers out there that are interested in the area of applied bioinformatics.

Come to our sessions as a simple listener, or become an active participant of this recurrent event and ask Dr. Kel your own questions in order to emphasise the direction of the live discussion.

You can send your questions via the form below or by email: with a subject “Question to Dr. Kel”.

Questions can also be asked live during the online event.



What to ask about?

Any question that you need assistance with while performing your bioinformatics analysis, e.g.

  • Promoter analysis? Pathway analysis?
  • Can AI analyze NGS data?
  • How to combine DNA methylation and metabolome data?
  • What to start from and how to interpret the obtained results?

and much more….


Check out the video records of the previous “Coffee break with TRANSFAC” sessions in order to find answers to the questions that have already been addressed.


17 January 2023, the first “Coffee break with TRANSFAC” session:



Your questions addressed within this session:

  • How can I start a TRANSFAC bioinformatics analysis? What types of data do I need?
  • What is the significance of a transcription factor binding site on plus or minus strand of the gene?
  • New transcription factors – do you survey those all the time? How many targets are necessary for inclusion of one (creation of a matrix) in the program?
  • What advantages does TRANSFAC have over the HOCOMOCO and JASPAR databases?
  • Regarding TF binding analysis: even after we get a putative motif for TFs, how many TF could possibly bind at a single site on the genome, depending on a significance cut-off, I find TF binding sites from 2-3 to almost 40-50 at the same location. How do we filter the noise or get accurate results?
  • Is it possible to use directly gene sequences to search TFBS? For example sequences from Ensembl database? FASTA file?
  • Either on + strand, or on – strand, one should read the binding site from 5′ end to 3′ end, is it correct?
  • Can a gene have two active promoters and corresponding TSS in the same cell?
  • In order to investigate how much a genetic mutation could affect a TF binding site, is it possible that such a mutation could affect multiple TFs binding at that region? Would it be advisable to focus only on TFs based on their binding score?
  • The co-occurrence of TFs proposed by TRANSFAC is based on the knowledge coming from different experiments, so what are the chances of co-occurrence actually?



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