geneXplain platform training

Training material for the usage of our geneXplain platform

Part 1 : Introduction

  1. How to navigate in the platform, how to search for information and how to load:
    – gene tables,
    – GEO database
  2. Filtering tables & annotate genes
  3. Data Normalization
  4. Principal Component Analysis
  5. Performing LIMMA – Differential Gene expression
  6. geneXplain Methods – convert different database identifiers.

1_Introduction_Exercises_2020

 

Part 2 : Identification of DNA motifs

Theory

  1. Gene regulation & Regulation of transcription
  2. TRANSFAC® DNA binding sites & DNA sequence motifs
  3. Positional Weight Matrix –binding site scores
  4. Binding site prediction & Identification of enriched motifs

2_Motif_finding_theory

Practical

  1. ChIPMunk in the geneXplain platform
  2. Binding site prediction in the geneXplain platform

2_Motif_finding_practical

 

Part 3 : Transcription Factors

Theory

  1. What are transcription factors?
  2. DNA binding domains
  3. Transcription Factor classification

3_Transcription_factors_theory

Practical

  1. Mapping a gene list with TF classification
  2. Converting Matrices to molecules
  3. Analyzing ChIP-seq peaks

3_Transcription_factors_practical

 

Part 4 : Enhancers

Theory

  1. What are enhancers?
  2. Promoter and enhancer
  3. Enhancers are site compositions = Composite Modules (CM)
  4. Search for Composite Modules (CM)
  5. Fantom5 Database

4_Enhancers_theory

Practical

  1. Identifying regulation specific combinations of transcription factor binding sites with the help of Composite Module Analysis (CMA)
  2. Using Fantom5 database to analyze tissue- or cell-type specific promoters

4_Enhancers_practical

 

Part 5 : Pathways

Coming soon …

Part 6 : Master regulators in networks

6_Networks_theory

 

Part 7 : Targets

Theory

  1. Upstream Analysis Concept
  2. Search for master regulators
  3. „Walking pathways“
  4. Upstream analysis – From motifs in promoters to drug targets
  5. Multi-omics data analysis
  6. Genomic variations in gene regulatory regions (regulatory SNPs)
  7. Druggability of the Master Regulators (drug targets)

7_Targets_theory

Practical

  1. Upstream analysis workflow in geneXplain platform
  2. Genome Enhancer software

7_Targets_practical

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