Old Tutorials¶
Tutorial 2.1. Sample Level Enrichment Analysis (SLEA) with KEGG pathways
- CASE STUDY: Studying the expression profile of 156 lung tumors and adjacent normal lung tissue samples
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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¶
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Tutorial 3.1 Gene Ontology enrichment analysis
Analyse the conservation patterns of genes involved in different biological processes
4. CASE STUDY 4: Studying the regulatory programs governing the expression in different tissues¶
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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
6. CASE STUDY: Studying multi-dimensional cancer data with Gitools¶
The videos we have put online for this case study we are accessible on Youtube.
Watch the whole case study as a YouTube playlist
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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
