Tutorials


Tutorial 2.1. Sample Level Enrichment Analysis (SLEA) with KEGG pathways

  1. 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

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Tutorial 2.2. Expression profiles correlations

Compare the expression profile of samples using correlations

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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

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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

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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

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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

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Tutorial 6.2. Finding and visualizing mutually exclusive genes

See which genes are altered in a mutually exclusive manner

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Tutorial 6.3. Exploring the effect of genomic alterations on expression

See which genes are significantly influenced by genomic alterations in their locus

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Tutorial 6.4: Sample Level Enrichment Analysis (SLEA)

Asses transcription level for pathways for each sample in the study