Differential Expression Analysis
The Differential Expression Analysis (
) and the Differential Expression Analysis from Count Matrix (
) template workflows can be used for performing differential expression analysis for gene or transcript expression data from groups of samples.
The workflows include all necessary steps for processing and analyzing the reads:
- Differentially expressed features (genes or transcripts) are identified using Differential Expression for RNA-Seq.
- The expression values are summarized in various plots using
- Terms from a Gene Ontology Annotation (GOA) table affected by the differentially expressed features are identified using Gene Set Test.
- The differentially expressed features are optionally uploaded to QIAGEN Ingenuity Pathway Analysis (IPA) using Upload to IPA.
The two workflows differ in the accepted inputs:
- Differential Expression Analysis takes as input Gene Expression (GE) or Transcript Expression (TE) tables or tracks. These must be associated with a CLC Metadata Table.
- Differential Expression Analysis from Count Matrix imports Gene Expression (GE) or Transcript Expression (TE) tracks, along with a CLC Metadata Table, from two separate files containing the expression data and metadata, respectively. See Import Expression Data for details.
Launching the workflows
To run these workflows, go to:
Workflows | Template Workflows | Biomedical Workflows (
) | Comparative Analysis (
)
and select:
Differential Expression Analysis ()
Differential Expression Analysis from Count Matrix ()
See Launching workflows individually and in batches for general information.
Options can be configured in the following dialogs:
- Choose where to run. If you are connected to a CLC Server via the CLC Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
- Specify workflow path. The following paths can be configured:
- Upload data to IPA. Select whether you want to upload the differential expression results to IPA. Uploading requires an IPA account.
- Additionally, for the "Differential Expression Analysis" workflow:
- RNA biotype. Select whether the samples to analyze contain expression data from RNA (excluding small RNA species) or miRNA.
- Select Expression tables or tracks, for the "Differential Expression Analysis" workflow. Select the Gene Expression (GE) or Transcript Expression (TE) tables or tracks to be analyzed.
- Specify reference data handling. Select the relevant Reference Data Set, see Reference data management for details.
- Import Expression Data, for the "Differential Expression Analysis from Count Matrix" workflow. Select the two files containing the expression data and metadata, respectively.
- Differential Expression for RNA-Seq/miRNA.
Configure the following options as needed:
- Metadata table
- Test differential expression due to
- While controlling for
- Comparisons
- Control group
- Filter on Custom Criteria, if "RNA" is selected as biotype in "Specify workflow path" or if running the "Differential Expression Analysis from Count Matrix" workflow. Configure filtering of the differential expression analysis results. See Filter on Custom Criteria for details.
- Upload to IPA, if "Upload data to IPA" is selected in "Specify workflow path". Login to IPA and configure the options. See Upload to IPA for details.
- Result handling. Choose if a workflow result metadata and/or log should be saved.
- Save location for new elements. Choose where to save the data, and press Finish to start the analysis.
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