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?
