Past Training Library

How to find tissue-specific TF target genes (16 Feb 2024)

Q&A, Coffee Break with TRANSFAC

Resources:

In this seminar Prof. Alexander Kel shared with you the latest intriguing insights into the mechanisms of gene regulation. He demonstrated how tissue-specific gene regulation analysis can be performed and how enriched motifs can be found using TRANSFAC database and its MATCH Suite component.

Key topics: 

  • How to find tissue-specific TF target genes?
  • Why do you need TF binding sites?
  • Conserved TF binding sites – how important are they?
  • PWMs – is that all? What else?

Answered questions:

  • How to find tissue-specific transcription factors regulating the selected genes from the tissue of your interest?
  • Position Weight Matrices (PWMs). Why they are important? What else can be used to find TF binding sites?
  • Does one PWM describe TF sites for one transcription factor only (e.g. STAT-1) or for the whole family of factors (STAT-1, STAT-2,….)? 
  • What are the algorithms for predicting TF binding sites in DNA based on positional weight matrices?    How to define the cut-offs for binding sites scores of PWMs?
  • In calculating FP (false positives) and FN (false negatives) you need to know the true binding sites. How are they determined?
  • Conserved TF binding sites. Are they the only true TF binding sites? How important are they? What is phylogenetic footprinting and how to use it while searching for TF binding sites that regulate the genes of your interest?
  • How to integrate transcriptome (RNA-seq) and epigenome (ATAC-seq) data in one TRANSFAC analysis?

Your first TRANSFAC analysis (23 Jan 2024)

Q&A, Coffee Break with TRANSFAC

Resources:

Key topics:

  • 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?

Answered questions:

  • How to find all target genes of NFkB transcription factor? 
  • MEF-2A transcription factor and its expression profile
  • Which TFs are regulating my genes specifically expressed in muscle tissue
  • MATCH Suite gene set analysis launch and results overview
  • Tissue-specific gene regulation
  • TFClass transcription factors classification
  • Expression patterns of transcription factors coming from one family
  • Constructing tissue specific gene set in MATCH Suite
  • Gene list optimization by GO terms in MATCH Suite
  • Heatmap of GO terms and TF motifs produced by MATCH Suite
  • MATCH Suite results overview from the geneXplain platform interface