Gene set enrichment analysis (Illumina probes) (workflow) - Revision history

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;Workflow title
:Gene set enrichment analysis (Illumina probes)
;Provider
:[[GeneXplain GmbH]]
== Workflow overview ==
[[File:Gene-set-enrichment-analysis-Illumina-probes-workflow-overview.png|400px]]
== Description ==
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 Transcript IDs or Illumina Gene 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 Illumina IDs and calculated fold change values is converted into a table with Ensembl Gene Ids

At 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.

For each ontological term several parameters are calculated, including nominal p-value, ES, NES, as well as hit names, the link to the corresponding ontological term, and the link to open a visualization plot.

== Parameters ==
;Experiment normalized
;Control normalized
;Species
;Results folder

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@@ 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.
-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.
 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
 ;Control normalized
 ;Species
 ;Results folder

@@ Line 6: / Line 6: @@
 [[File:Gene-set-enrichment-analysis-Illumina-probes-workflow-overview.png|400px]]
 == Description ==
-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”.
+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.
-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.
+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.
-At the next step, the Ensembl genes are annotated with additional information, gene description and gene symbols.
+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.
-−
-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.
-−
-For each ontological item several parameters are calculated, including nominal p-value, ES, NES, as well as hit names, the link to the corresponding ontological term, and the link to open a visualization plot.
-−
-−
 == Parameters ==

@@ Line 6: / Line 6: @@
 [[File:Gene-set-enrichment-analysis-Illumina-probes-workflow-overview.png|400px]]
 == Description ==
-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”.
-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.
+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.
-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.
+At the next step, the Ensembl genes are annotated with additional information, gene description and gene symbols.
 == Parameters ==

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 :Gene set enrichment analysis (Illumina probes)
 ;Provider
-:[[GeneXplain GmbH]]
+:[[geneXplain GmbH]]
 == Workflow overview ==
 [[File:Gene-set-enrichment-analysis-Illumina-probes-workflow-overview.png|400px]]