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Michael P Schroeder
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Case Study 1
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‎.gitignore‎

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# Maven files
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target/
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# Operating System annoyances
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*.DS_Store

‎doc/Tutorials.rst‎

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`CASE STUDY 1: Finding the Biological Processes enriched among genes significantly up-regulated in different types of cancer <#HCASESTUDY1:FindingtheBiologicalProcesse>`__
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`CASE STUDY 2: Studying the expression profile of 156 lung tumors and adjacent normal lung tissue samples <#HCASESTUDY2:Studyingtheexpressionprofile>`__
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`CASE STUDY 3: Functional protein divergence in the evolution of Homo sapiens <#HCASESTUDY3:Functionalproteindivergencei>`__
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`CASE STUDY 4: Studying the regulatory programs governing the expression in different tissues <#HCASESTUDY4:Studyingtheregulatoryprogram>`__
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`CASE STUDY 5: Experimental regulatory modules in cancer <#HCASESTUDY5:Experimentalregulatorymodule>`__
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`CASE STUDY 6: Studying multi-dimensional cancer data with Gitools <#HCASESTUDY6:Studyingmulti-dimensionalcan>`__
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.. contents::
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CASE STUDY 1: Finding the Biological Processes enriched among genes significantly up-regulated in different types of cancer
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Import a data matrix from IntOGen that contains p-values for significantly up-regulated genes in each tumor morphology type
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Import a module file that maps all human genes to KEGG Pathways and the annotations of these terms
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.. list-table:: Case study 1:
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Run an enrichment analysis to test which pathways are enriched among genes significantly up-regulated in different types of cancer
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Explore the heatmap with the enrichment analysis results by sorting, filtering, hiding and moving rows and columns
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Edit properties of the heatmaps: change color scale, add annotations, change font size and edit grid
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Export the results of the enrichment analysis as an image and as a table containing the details of the statistic results
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* - .. image:: img/tutorial-icon1-1.png
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- `Tutorial 1.1: Import Data Matrix From IntOGen <pdf/tutorial11importintogentumortypes.pdf>`_
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Import a data matrix from IntOGen that contains p-values for significantly up-regulated genes in each tumor morphology type
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* - .. image:: img/tutorial-icon1-2.png
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- `Tutorial 1.2: Import pathways From KEGG <pdf/tutorial12importensemblKEGG.pdf>`_
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Import a module file that maps all human genes to KEGG Pathways and the annotations of these terms
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* - .. image:: img/tutorial-icon1-3.png
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- `Tutorial 1.3: Run Enrichment Analysis <pdf/tutorial13runenrichmentIntOGenKEGG.pdf>`_
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Run an enrichment analysis to test which pathways are enriched among genes significantly up-regulated in different types of cancer
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* - .. image:: img/tutorial-icon1-4.png
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- `Tutorial 1.4: Explore results in a heatmap <pdf/tutorial14exploreresultsIntOGenKEGG.pdf>`_
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Explore the heatmap with the enrichment analysis results by sorting, filtering, hiding and moving rows and columns
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* - .. image:: img/tutorial-icon1-5.png
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- `Tutorial 1.5: Edit heatmaps <pdf/tutorial15editheatmaps.pdf>`_
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Edit properties of the heatmaps: change color scale, add annotations, change font size and edit grid
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* - .. image:: img/tutorial-icon1-6.png
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- `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
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CASE STUDY 2: Studying the expression profile of 156 lung tumors and adjacent normal lung tissue samples
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