Tutorial 2.1. Sample Level Enrichment Analysis (SLEA) with KEGG pathways
Identify pathways which genes are differentially expressed in various groups of samples
We will use a data set containing 156 non-small cell lung carcinomas and adjacent normal lung tissue sample from Hou et al 2010 .
Use annotations for pathways and annotation colors for samples
- In the analysis details tab, click on heatmap under Results to view the heatmap of the results.
- Change the color scale to z-score scale in the properties/cells tab under “scale”.
- In properties/rows, select the file homo_sapiens_kegg_pathways_ensembl_affy_hg_u133_plus_2_annotations.tsv and choose “name” as label to show the name of the pathways instead of the id in the heatmap.
- In properties/columns, select the file “gse19188_sample_annotations.txt” and choose “histology” as label to show the type of tumour instead of the id of the sample as column name in the heatmap.
- Select annotate with color to show a color label for the type of histology of the samples.
- Sort the samples by histology by selecting Data>Sort>Sort by label and select columns.
- Change the width of the cells in properties/cells to be able to see all the samples in the window and uncheck the option to show the columns grid.
Explore the results