Difference between revisions of "Gene set enrichment analysis (Illumina probes) (workflow)"
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
||
| (8 intermediate revisions by one user not shown) | |||
| Line 2: | Line 2: | ||
:Gene set enrichment analysis (Illumina probes) | :Gene set enrichment analysis (Illumina probes) | ||
;Provider | ;Provider | ||
| − | :[[ | + | :[[geneXplain GmbH]] |
== Workflow overview == | == Workflow overview == | ||
[[File:Gene-set-enrichment-analysis-Illumina-probes-workflow-overview.png|400px]] | [[File:Gene-set-enrichment-analysis-Illumina-probes-workflow-overview.png|400px]] | ||
== Description == | == 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]. | + | 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 | + | 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. | 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. | |
== Parameters == | == Parameters == | ||
;Experiment normalized | ;Experiment normalized | ||
;Control normalized | ;Control normalized | ||
| + | ;Annotation source | ||
;Species | ;Species | ||
;Results folder | ;Results folder | ||
[[Category:Workflows]] | [[Category:Workflows]] | ||
| + | [[Category:GeneXplain workflows]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 16:34, 12 March 2019
- Workflow title
- Gene set enrichment analysis (Illumina probes)
- Provider
- geneXplain GmbH
[edit] Workflow overview
[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
