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| = Protocol = * A to Z protocol to create an EnrichmentMap from gene expression data and using GSEA (Gene Set Enrichment Map) |
= A to Z protocol to create an EnrichmentMap from gene expression data and using GSEA (Gene Set Enrichment Analysis) = * goal (waht is the goal of enrichment analysis) * specific goal: known all pathways that could be altered between the 2 (or more) conditions that we are testing. We aim in this analysis to have a global and comprehensive view of what is happening in the cells. Snapshots of entire cells at the moment the RNA was extracted. |
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| == Installation == == How to preprocess the data using R == * 1) install R : * 2) install RStudio : == How to preprocess the data using Excel == |
* How to create a rank file (.rnk) * the rank file contains only 2 columns. The gene names as the first column and the differential expression values for each gene as the second column. In this protocol, we will use the t value from a moderated Student's t-test. Headers (column names) should be removed. The format should be tab delimited (meaning that the columns are separated by tabs) and the file extension should be .rnk. * the rank file is a format described in the GSEA documentation: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats * the rank file will be used to run the gene set enrichment analysis (GSEA). * How to get the pathway database file (.gmt) * * In this protocol we are going to use a file that include pathways from different sources. We observed that having the most comprehensive set of pathways gave more sensitive results. Although databases that are included in this file can be overlapping, they are not 100% identical -thus using several give more sensitivity - and the clusters created by the enrichment map from these different sources add confidence about the perturbation of a given biological function. * The link to the database file compilded by the BaderLab and updated monthly can be found at : * How to run GSEA * How to create an expression file * How to create a map * What is the next step, how to use the map * How to create a figure * How to interpret the results * What next * (How to preprocess the data using R) * (How to preprocess the data using Excel) = FIRST EXAMPLE WITH AFFYMETRIX MICROARRAY DATA = * description of the data == Download the data from GEO == == Installation == * 1) install R (http://www.r-project.org/) * 2) install RStudio (http://www.rstudio.com/) * 3) Go through on online R tutorial (e.g. this one: http://www.cyclismo.org/tutorial/R/) == How to preprocess the data (normalization, QC, differential expression) == == How to update the annotations == |
A to Z protocol to create an EnrichmentMap from gene expression data and using GSEA (Gene Set Enrichment Analysis)
- goal (waht is the goal of enrichment analysis)
- specific goal: known all pathways that could be altered between the 2 (or more) conditions that we are testing. We aim in this analysis to have a global and comprehensive view of what is happening in the cells. Snapshots of entire cells at the moment the RNA was extracted.
- How to create a rank file (.rnk)
- the rank file contains only 2 columns. The gene names as the first column and the differential expression values for each gene as the second column. In this protocol, we will use the t value from a moderated Student's t-test. Headers (column names) should be removed. The format should be tab delimited (meaning that the columns are separated by tabs) and the file extension should be .rnk.
the rank file is a format described in the GSEA documentation: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
- the rank file will be used to run the gene set enrichment analysis (GSEA).
- How to get the pathway database file (.gmt)
- In this protocol we are going to use a file that include pathways from different sources. We observed that having the most comprehensive set of pathways gave more sensitive results. Although databases that are included in this file can be overlapping, they are not 100% identical -thus using several give more sensitivity - and the clusters created by the enrichment map from these different sources add confidence about the perturbation of a given biological function.
The link to the database file compilded by the BaderLab and updated monthly can be found at :
- How to run GSEA
- How to create an expression file
- How to create a map
- What is the next step, how to use the map
- How to create a figure
- How to interpret the results
- What next
- (How to preprocess the data using R)
- (How to preprocess the data using Excel)
FIRST EXAMPLE WITH AFFYMETRIX MICROARRAY DATA
- description of the data
Download the data from GEO
Installation
1) install R (http://www.r-project.org/)
2) install RStudio (http://www.rstudio.com/)
3) Go through on online R tutorial (e.g. this one: http://www.cyclismo.org/tutorial/R/)
How to preprocess the data (normalization, QC, differential expression)
How to update the annotations
How to create a rank file
How to create an expression file
How to run GSEA
How to create a map