Difference between revisions of "Gene set enrichment analysis (Illumina probes) (workflow)"

From BioUML platform
Jump to: navigation, search
(Automatic synchronization with BioUML)
(Automatic synchronization with BioUML)
 
Line 8: Line 8:
 
This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at  [http://www.broadinstitute.org/gsea/index.jsp http://www.broadinstitute.org/gsea/index.jsp].  As input, the normalized data with Illumina probeset IDs can be submitted.
 
This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at  [http://www.broadinstitute.org/gsea/index.jsp http://www.broadinstitute.org/gsea/index.jsp].  As input, the normalized data with Illumina probeset IDs can be submitted.
  
−
Such normalized files are resulting from the “Normalize data” procedure under “Analyses/Methods/Data normalization/Normalize Illumina experiment and control”. First, the input files are subjected to fold-change calculation. The table with probeset IDs and calculated fold change values is converted into a table with Ensembl Gene IDs. In the next step, the Ensembl genes are annotated with additional information, gene description and gene symbols.
+
Such normalized files are resulting from the “Normalize data” procedure under “Analyses/Methods/Data normalization/Normalize Illumina experiment and control”. First, the input files are subjected to fold-change calculation.
  
−
Finally the annotated Ensembl genes are subjected to GSEA using the PROTEOME<sup>TM</sup> database. Enrichment analysis is performed using the following ontologies: PROTEOME GO biological processes, PROTEOME GO cellular components, PROTEOME GO molecular function, PROTEOME disease and by the TRANSPATH pathways.
+
 The table with probeset IDs and calculated fold change values is converted into a table with Ensembl Gene IDs. In the next step, the Ensembl genes are annotated with additional information, gene description and gene symbols.
 +
 
 +
Finally the annotated Ensembl genes are subjected to GSEA. Enrichment analysis is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions and by the Reactome pathways.
  
 
Output files include enrichment analysis results, a list of annotated Ensemble genes and a histogram of log fold change distribution. For each ontological term several parameters are calculated, including nominal p-value, ES, NES, FDR, rank at max, hit names, the link to the corresponding ontological term, and the link to open a visualization plot.
 
Output files include enrichment analysis results, a list of annotated Ensemble genes and a histogram of log fold change distribution. For each ontological term several parameters are calculated, including nominal p-value, ES, NES, FDR, rank at max, hit names, the link to the corresponding ontological term, and the link to open a visualization plot.
Line 17: Line 19:
 
;Experiment normalized
 
;Experiment normalized
 
;Control normalized
 
;Control normalized
 +
;Annotation source
 
;Species
 
;Species
 
;Results folder
 
;Results folder

Latest revision as of 16:34, 12 March 2019

Workflow title
Gene set enrichment analysis (Illumina probes)
Provider
geneXplain GmbH

[edit] Workflow overview

Gene-set-enrichment-analysis-Illumina-probes-workflow-overview.png

[edit] Description

This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at  http://www.broadinstitute.org/gsea/index.jsp.  As input, the normalized data with Illumina probeset IDs can be submitted.

Such normalized files are resulting from the “Normalize data” procedure under “Analyses/Methods/Data normalization/Normalize Illumina experiment and control”. First, the input files are subjected to fold-change calculation.

 The table with probeset IDs and calculated fold change values is converted into a table with Ensembl Gene IDs. In the next step, the Ensembl genes are annotated with additional information, gene description and gene symbols.

Finally the annotated Ensembl genes are subjected to GSEA. Enrichment analysis is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions and by the Reactome pathways.

Output files include enrichment analysis results, a list of annotated Ensemble genes and a histogram of log fold change distribution. For each ontological term several parameters are calculated, including nominal p-value, ES, NES, FDR, rank at max, hit names, the link to the corresponding ontological term, and the link to open a visualization plot.

[edit] Parameters

Experiment normalized
Control normalized
Annotation source
Species
Results folder
Retrieved from "https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_(Illumina_probes)_(workflow)&oldid=7853"
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox