The twenty seventh coffee break with TRANSFAC

This video is a record of the live session "The twenty seventh Coffee break with TRANSFAC" that was held on 18th of June 2024.
The event was hosted by Dr. Alexander Kel, CEO of geneXplain GmbH.
The aim of this series of recurrent events titled as "Coffee break with TRANSFAC" is to provide answers to the questions of our audience in regards to the field of applied bioinformatics.
You can find further info about the "Coffee break with TRANSFAC" initiative at genexplain.com...
The list of questions that were addressed within this session and their time codes:
00:56 Why prediction of interactions between TFs and their binding sites needs to be done if you don’t want to miss the molecular mechanisms you are studying during pathway analysis
03:46 Example from GSE222916 (www.ncbi.nlm.n...)
Gene expression of fibroblasts treated with TGFβ (transformation to fibrosis)
10:20 Pathway analysis tools on the example of REACTOME, KEGG, PANTHER DB and CPDR from Max Planck Institute for Molecular Genetics - allowing to identify secondary effects (downstream analysis) but not the causative targets of the observed process (upstream analysis)
14:57 Why standard pathway enrichment analysis won’t allow you to identify the original changes? Variability of the target gene sets depending on the tissue or cell type. Necessity of predicting the target genes for the given conditions (pathways stop at the level of TFs)
19:27 Key principles of search for master regulators
29:39 The concept of Walking Pathways (pathway rewiring)
33:17 Genome Enhancer tool for master regulator search (Upstream Analysis)
35:02 Launching Genome Enhancer on raw gene counts data from GSE222916 (www.ncbi.nlm.n...)
40:45 Genome Enhancer analysis results overview
42:05 Do we give input to Genome Enhancer as raw counts or the upregulated and downregulated genes separately?
48:51 Another example where two omics types (transcriptomics and proteomics) are integrated in one analysis (based on the data from PMID 26538417 pubmed.ncbi.nl.... Osteosarcoma was studied at Myc activation. Proteome appeared to be correlating with transcriptome in this experiment.
01:00:08 Is it possible to analyze the structure of promoter, like which sequence is necessary and which is dispensable?