geneXplain platform training
Training material for the usage of our geneXplain platform
Part 1 : Introduction
- How to navigate in the platform, how to search for information and how to load:
– gene tables,
– GEO database - Filtering tables & annotate genes
- Data Normalization
- Principal Component Analysis
- Performing LIMMA – Differential Gene expression
- geneXplain Methods – convert different database identifiers.
Part 2 : Identification of DNA motifs
Theory
- Gene regulation & Regulation of transcription
- TRANSFAC® DNA binding sites & DNA sequence motifs
- Positional Weight Matrix –binding site scores
- Binding site prediction & Identification of enriched motifs
Practical
- ChIPMunk in the geneXplain platform
- Binding site prediction in the geneXplain platform
Part 3 : Transcription Factors
Theory
- What are transcription factors?
- DNA binding domains
- Transcription Factor classification
3_Transcription_factors_theory
Practical
- Mapping a gene list with TF classification
- Converting Matrices to molecules
- Analyzing ChIP-seq peaks
3_Transcription_factors_practical
Part 4 : Enhancers
Theory
- What are enhancers?
- Promoter and enhancer
- Enhancers are site compositions = Composite Modules (CM)
- Search for Composite Modules (CM)
- Fantom5 Database
Practical
- Identifying regulation specific combinations of transcription factor binding sites with the help of Composite Module Analysis (CMA)
- Using Fantom5 database to analyze tissue- or cell-type specific promoters
Part 5 : Pathways
Coming soon …
Part 6 : Master regulators in networks
Part 7 : Targets
Theory
- Upstream Analysis Concept
- Search for master regulators
- „Walking pathways“
- Upstream analysis – From motifs in promoters to drug targets
- Multi-omics data analysis
- Genomic variations in gene regulatory regions (regulatory SNPs)
- Druggability of the Master Regulators (drug targets)
Practical
- Upstream analysis workflow in geneXplain platform
- Genome Enhancer software