The Ingenuity Pathway Analysis plugin provides the ability to upload Statistical comparison data generated using the RNA-Seq tools from CLC Genomics Workbench to Ingenuity Pathway Analysis (IPA). In addition it provides support for import of expression data provided as a count matrix.

IPA provides valuable biological insight into the results of gene expression experiments by uncovering enriched signaling and metabolic pathways, activated and inhibited upstream regulators and effects on downstream diseases, functions, and phenotypes. IPA can visualize at the isoform level for human genes.

The plugin comes with two tools and two template workflows (figure 1.1):

Image IPA-plugin-tools-in-action-tree
Figure 1.1: IPA plugin tools and workflow when installed in the CLC Genomics Workbench Toolbox.

It is possible to use gene and transcript based RNA-Seq experiments as basis for the analysis, but also microarrays from Illumina and Affymetrix are supported. You can also upload small RNA based experiments (Statistical Comparison Table format) where the seeds are most appropriate to upload.

Once the experiment data are ready, it is possible to annotate with any of the supported statistics: