CASE STUDY 1: Finding the Biological Processes enriched among genes significantly up-regulated in different types of cancer

	Tutorial 1.1: Import Data Matrix From IntOGen Import a data matrix from IntOGen that contains p-values for significantly up-regulated genes in each tumor morphology type
	Tutorial 1.2: Import pathways From KEGG Import a module file that maps all human genes to KEGG Pathways and the annotations of these terms
	Tutorial 1.3: Run Enrichment Analysis Run an enrichment analysis to test which pathways are enriched among genes significantly up-regulated in different types of cancer
	Tutorial 1.4: Explore results in a heatmap Explore the heatmap with the enrichment analysis results by sorting, filtering, hiding and moving rows and columns
	Tutorial 1.5: Edit heatmaps Edit properties of the heatmaps: change color scale, add annotations, change font size and edit grid
	Tutorial 1.6: Export heatmap image and table results Export the results of the enrichment analysis as an image and as a table containing the details of the statistic results

CASE STUDY 2: Studying the expression profile of 156 lung tumors and adjacent normal lung tissue samples

	Tutorial 2.1: Sample Level Enrichment Analysis (SLEA) with KEGG pathways Identify pathways which genes are differentially expressed in various groups of samples
	Tutorial 2.2: Expression profiles correlations Compare the expression profile of samples using correlations
	Tutorial 2.3: Identifying significantly up-regulated genes Run Oncodrive to identify the genes that are significantly up-regulated taking into account a set of tumour samples
	Tutorial 2.4: Compare and combine experiments Compare and combine the significantly up-regulated genes in our experiment and other lung experiments imported from IntOGen
	Tutorial 2.5: Overlapping analysis Compare the overlap of significantly up-regulated genes in our experiment and in other lung experiments imported from IntOGen

Tutorial 3.1: Gene Ontology enrichment analysis
Analyse the conservation patterns of genes involved in different biological processes

	Tutorial 4.1: TFBS enrichment analysis Identify the transcription factors involved in the regulation of expression in different tissues
	Tutorial 4.2. Correlation of expression patterns in different tissues Compare the expression pattern of genes expressed in different tissues

Study the misregulation in different cancer types of modules derived from binding experiments such as ChIP-sequencing

The videos we have put online for this case study we are accessible on Youtube.
Watch the whole case study as a YouTube playlist

	Tutorial 6.1. Loading and annotating a multi-value matrix Get prepared to start working
	Tutorial 6.2. Finding and visualizing mutually exclusive genes See which genes are altered in a mutually exclusive manner
	Tutorial 6.3. Exploring the effect of genomic alterations on expression See which genes are significantly influenced by genomic alterations in their locus
	Tutorial 6.4. Sample Level Enrichment Analysis Asses transcription level for pathways for each sample in the study