Don’t do pathway analysis without TRANSFAC

Q&A: Coffee break with TRANSFAC

This event was held on 18 June , 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 you the Upstream Analysis approach that combines robust TRANSFAC TF binding site search with the fine pathway database TRANSPATH for reconstructing the key pathways and finding master regulators in them. You will learn how to use easy online tools that will automatically analyze your gene list, build specific gene regulatory and signal transduction pathway, find master regulators, and produce nice network visualizations ready for your paper.

You’ve got your gene list from RNA-seq and would like to find key pathways acting in the disease you study. You are going to use pathway databases, such as Reactome, KEGG or BioCyc to do the pathways analysis. 

You still may miss the key pathway acting in your cells under study if you don’t use TRANSFAC. More than 99% of true TF-DNA interactions are missing in the pathway databases. 

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

  • Master regulators controlling the activity of transcription factors
  • Walking pathways: pathway rewiring
  • Integrated transcriptomics and proteomics analysis of Myc-induced U2OS cells (data from PMID: 26538417)
  • Visualization of signalling pathways and networks

What you will learn in this webseminar 

  • How can I identify master regulators governing the the transcription factors in focus?
  • Which databases to use? HumanPSD+TRANSPATH and other databases.
  • Graph search algorithms. Master regulators with positive feedback loops.
  • Integration of transcriptomics and proteomics data in one analysis for identification of prospective drug targets and biomarkers
  • Visualization of TRANSPATH pathways in Cytoscape

Seminar Schedule

The session was held on June 18th, it started 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).

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 and their regulators

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+HumanPSD+TRANSPATH 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 account.

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