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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::
    :widths: 30 70

    * - .. image:: img/tutorial-icon1-1.png
      - Tutorial 1.1: Import Data Matrix From IntOGen :download:`download pdf<files/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 :download:`download pdf<files/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 :download:`download pdf<files/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 :download:`download pdf<files/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 :download:`download pdf<files/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 :download:`download pdf<files/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::
    :widths: 30 70

    * - .. 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:: 
    :widths: 30 70

    * - .. 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::
    :widths: 30 70

    * - .. 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::
    :widths: 30 70

    * - .. 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::
    :widths: 30 70

    * - .. 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
