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Tutorials
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.. contents::

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

  * - .. image:: img/tutorial-icon1-1.png
    - `Tutorial 1.1: Import Data Matrix From IntOGen <pdf/tutorial11importintogentumortypes.pdf>`_
      
      Import a data matrix from IntOGen that contains p-values for significantly up-regulated genes in each tumor morphology type
  
  * - .. image:: img/tutorial-icon1-2.png
    - `Tutorial 1.2: Import pathways From KEGG <pdf/tutorial12importensemblKEGG.pdf>`_
      
      Import a module file that maps all human genes to KEGG Pathways and the annotations of these terms
  
  * - .. image:: img/tutorial-icon1-3.png
    - `Tutorial 1.3: Run Enrichment Analysis <pdf/tutorial13runenrichmentIntOGenKEGG.pdf>`_
       
      Run an enrichment analysis to test which pathways are enriched among genes significantly up-regulated in different types of cancer
  
  * - .. image:: img/tutorial-icon1-4.png
    - `Tutorial 1.4: Explore results in a heatmap <pdf/tutorial14exploreresultsIntOGenKEGG.pdf>`_
     
      Explore the heatmap with the enrichment analysis results by sorting, filtering, hiding and moving rows and columns
  
  * - .. image:: img/tutorial-icon1-5.png
    - `Tutorial 1.5: Edit heatmaps <pdf/tutorial15editheatmaps.pdf>`_
       
      Edit properties of the heatmaps: change color scale, add annotations, change font size and edit grid
  
  * - .. image:: img/tutorial-icon1-6.png
    - `Tutorial 1.6: Export heatmap image and table results <pdf/tutorial16exportheatmaps.pdf>`_ 
      
      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
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.. list-table:: 

  * - .. image:: img/tutorial-iconCS2.1.png
    - :doc:`Tutorials_Tutorial21` 
      
      Identify pathways which genes are differentially expressed in various groups of samples

  * - .. image:: img/tutorial-iconCS2.2.png
    - :doc:`Tutorials_Tutorial22` 
      
      Compare the expression profile of samples using correlations

  * - .. image:: img/tutorial-iconCS2.3.png
    - :doc:`Tutorials_Tutorial23` 
      
      Run Oncodrive to identify the genes that are significantly up-regulated taking into account a set of tumour samples

  * - .. image:: img/tutorial-iconCS2.4.png
    - :doc:`Tutorials_Tutorial24` 
      
      Compare and combine the significantly up-regulated genes in our experiment and other lung experiments imported from IntOGen

  * - .. image:: img/tutorial-iconCS2.5.png
    - :doc:`Tutorials_Tutorial25` 
      
      Compare the overlap of significantly up-regulated genes in our experiment and in other lung experiments imported from IntOGen



CASE STUDY 3: Functional protein divergence in the evolution of Homo sapiens
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.. list-table:: 


  * - .. image:: img/tutorial-iconCS3.1.png
    - :doc:`Tutorials_Tutorial31` 
      
      Analyse the conservation patterns of genes involved in different biological processes                                                                          


CASE STUDY 4: Studying the regulatory programs governing the expression in different tissues
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.. list-table:: 

  * - .. image:: img/tutorial-icon1.png
    - :doc:`Tutorials_Tutorial41` 
      
      Identify the transcription factors involved in the regulation of expression in different tissues                                                                       

  * - .. image:: img/tutorial-icon2.png
    - :doc:`Tutorials_Tutorial42` 
      
      Compare the expression pattern of genes expressed in different tissues                                                                                                                                              





CASE STUDY 5: Experimental regulatory modules in cancer
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.. list-table:: 

  * - .. image:: img/tutorial-icon3.png
    - :doc:`Tutorials_Tutorial51` 
      
      Study the misregulation in different cancer types of modules derived from binding experiments such as ChIP-sequencing                                                                       





CASE STUDY 6: Studying multi-dimensional cancer data with Gitools
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The videos we have put online for this case study we are accessible on Youtube.

**Watch the whole case study as a** `YouTube playlist <http://www.youtube.com/playlist?list=PLE1820A1F67A7407E&feature=view_all>`_ 

.. list-table:: 

  * - .. image:: img/tutorial-icon6-1.png
    - :doc:`Tutorials_Tutorial61` 
      
      Get prepared to start working

  * - .. image:: img/tutorial-icon6-2.png
    - :doc:`Tutorials_Tutorial62` 
      
      See which genes are altered in a mutually exclusive manner

  * - .. image:: img/tutorial-icon6-3.png
    - :doc:`Tutorials_Tutorial63` 
      
      See which genes are significantly influenced by genomic alterations in their locus

  * - .. image:: img/tutorial-icon6-4.png
    - :doc:`Tutorials_Tutorial64` 
      
      Asses transcription level for pathways for each sample in the study


