Tutorials¶

CASE STUDY: 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 upregulated 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

3. CASE STUDY : Functional protein divergence in the evolution of Homo sapiens¶

Analyse the conservation patterns of genes involved in different biological processes

Identify the transcription factors involved in the regulation of expression in different tissues

Compare the expression pattern of genes expressed in different tissues

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 (SLEA) Asses transcription level for pathways for each sample in the study