Your first TRANSFAC analysis

Q&A: Coffee break with TRANSFAC

Event was held on 16th of April, 2024

FREE online seminar

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Seminar Description

In this webinar Dr. Alexander Kel, the CEO and CSO of geneXplain GmbH, will introduce to you the basic principles of promoter analysis and identification of transcription factor binding sites. You will learn how to use TRANSFAC and perform your first steps towards the understanding of gene regulation. 

The following main questions will be in the focus at this seminar:

  • Transcription factors. Why they are important?
  • What are DNA binding motifs? TRANSFAC and JASPAR.
  • How to analyse promoters? Match and HOMER.
  • How to start and how to interpret the obtained results?

What you will learn in this webseminar 

  • How can I start a TRANSFAC bioinformatics analysis? What types of data do I need?
  • Which databases to use? TRANSFAC and other databases.
  • What advantages does TRANSFAC have over the HOCOMOCO and JASPAR databases?
  • Algorithms to find TF binding sites. Match and HOMER.
  • 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?
  • 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 the significance cut-off, from 2-3 to almost 40-50 TF binding sites can be found at the same location. How do we filter the noise or get accurate results?
  • Is it possible to use directly gene sequences to search for 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?
  • 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?

Seminar Schedule

The session was held on April 16, 2024 with a lecture from Prof. Alexander Kel (approx. 1 hour) and was continued with a Q&A session addressing the questions coming from the attendees of the online event (approx. 30 minutes).

Information resources

What You Get

  • 1 hour lecture on gene regulation analysis provided by one of the key opinion makers in this field
  • 30 minutes interactive Q&A session addressing your questions regarding search for TFBS
  • Time-unlimited access to the video record of the session
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The Lecturer

  • Alexander Kel received his Ph.D. in Bioinformatics, Molecular Biology and Genetics in 1990 and has has over 35 years of research experience in Bioinformatics
  • He studied at Novosibirsk State University, obtaining an M.S. in biology with a focus on mathematical biology in 1985
  • His work spans numerous bioinformatics branches (sequence analysis, gene recognition, promoter/enhancer analysis and prediction, prediction of RNA secondary structure, analysis of signal transduction pathways, identification of drug targets, systems biology and systems medicine)
  • He is the originator of the “fuzzy puzzle” concept for gene regulatory regions modeling
  • Developed “upstream analysis” for identifying biomarkers and drug targets in various diseases
  • Participated in over 20 national and international research projects
  • Author of more than 130 scientific publications and several book chapters on bioinformatics and systems biology
  • CEO and CSO of geneXplain GmbH, Wolfenbüttel, Germany
  • Visiting Professor at Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland

Prerequisites

Basic knowledge of biochemistry and molecular biology. No programming skills are required.

To Whom It Might Be Interesting

  • Bench biologists seeking for ways to deal with sequencing data in order to discover what is hidden there in terms of genes, promoters, and repressors

FAQ

That’s ok! All registered course attendees will receive access to the video record of the session together with the presentation materials. 

You can ask your questions live during the online event using the Q&A section of the online webinar, or you can send us your questions in advance using the form on this page and Prof. Dr. Alexander Kel will address them at the online event.

Sure! All licensed TRANSFAC users will be able to repeat all steps of the analysis that will be shown by Prof. Dr. Alexander Kel during the online event using their geneXplain platform and TRANSFAC accounts.

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