TRANSFAC download

Software demo: Coffee break with TRANSFAC

May 28th, 10 AM CEST

FREE online seminar

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Seminar Description

Download TRANSFAC and do whatever you like

Introduction to the TRANSFAC flat file download release

Download TRANSFAC and do whatever you like

TRANSFAC® (including TRANSCompel® and TANSPro™) contains eukaryotic transcription factors (and miRNAs), their experimentally determined genomic binding sites and consensus DNA-binding motifs (PWMs), as well as data on combinatorial gene regulation and factor-factor interaction.

Promoters, enhancers and silencers annotated with transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project and from other sources complement the manually curated binding site data. 

Based on the positional weight matrices (PWMs) transcription factor binding sites can be predicted in regulatory regions (with Match™).

In the TRANSFAC® flat file download, the Match™ tool can be used in the command line or the PWMs can be used with third-party tools or with tools of the user.

This webseminar will give a brief overview of TRANSFAC® with the focus on the flat file download release.

The following main topics will be in the focus of this webseminar:

  • Factor-site binding
  • Factor-factor interaction
  • Combinatorial gene regulation
  • Gene regulatory networks
  • Promoters & Enhancers
  • Factor classification
  • TF-binding motifs (PWMs)
  • TF-binding site prediction

What you will learn in this webseminar 

  • Content of TRANSFAC
  • Data structure of the TRANSFAC flat files
  • Differences between the download and the online release
  • TF-consensus binding motifs in the form of PWMs
  • TF-binding site prediction using the command line with the Java Match Library

Seminar Schedule

The session will start on May 28 with a lecture and software demo from Dr. Volker Matys and Kamilya Altynbekova (approx. 1 hour) and will be continued with a Q&A session addressing the questions coming from the attendees of the online event (up to 30 minutes).

What You Get

  • 1 hour lecture and software demo on gene regulation analysis provided by TRANSFAC experts
  • 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 Lecturers

Prof. Dr. Alexander Kel

  • 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
Kamilya Altynbekova

Kamilya Altynbekova

  • Blending her Computer Science background with a passion for life sciences, Kamilya Altynbekova works as software developer at geneXplain
  • Kamilya’s main responsibility is the development for geneXplain platform, maintenance of the existing tools and integration of the new analysis
  • As a part of geneXplain team, Kamilya also participates in research projects by conducting data analysis to extract valuable insights from biological data, often dealing with large datasets
Dr. Volker Matys

Dr. Volker Matys

  • Dr. Volker Matys, graduated in Biology at the University of Freiburg, Germany with a thesis in Molecular Biology (based on experimental research conducted at St. George’s Hospital Medical School, London)
  • Volker has been working on TRANSFAC for more than twenty years in various functions, initially as a database curator and editor, and later in quality control and customer support

Prerequisites

Basic knowledge of biochemistry and molecular biology. Being familiar with the use of Java-based or other command line tools. Data extraction from the flat files requires programming skills (or SQL).

To Whom It Might Be Interesting

  • Bioinformaticians who want to extract data on gene regulation for use with the included command line tools or with their own or third-party tools.

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 our experts will address them at the online event.

Sure! All duly licensed TRANSFAC download users will be able to repeat all steps of the analysis that will be shown by our experts during the online event.

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