==============
Old Tutorials
==============

.. contents::

 1. Tutorial: Gitools from A to Z
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:doc:`Tutorials_Tutorial21`



 2. CASE STUDY: 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


3. CASE STUDY : 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

4. 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

6. CASE STUDY: 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