IPA Winter Release 2015

What’s New in the IPA Winter Release (December 2015)

Gain more insight by customizing pathway and network overlays

Now you can choose which measurement to overlay on networks and pathways from your dataset or analysis, and then quickly customize the range of color to emphasize the genes of interest.


Fig 1. See the expression more clearly. In this Canonical Pathway overlaid with an analysis of RNA-Seq data, the range of gene expression fold changes from the analysis has been user specified with IPA’s new range slider. This is especially important in datasets with a large range of fold changes (typical for RNA-Seq), where the default scaling often leads to nodes that are very pale in color, even when they have fairly large fold change values.


Fig 2. See the significance. For the first time in IPA, you can easily switch which measurement values are visually overlaid from a dataset or analysis. The pictured Canonical Pathway was overlaid with an analysis with the default fold change, and then the overlay was switched to visualize the p-value with a red fill. This helps you see which nodes are the most significant and then toggle the overlay back to fold change if desired.


Fig 3. Simple multi-omics overlay. The ability to switch overlays makes it simple to visualize expression data versus variant gain/loss values. The screenshot on the left shows an expression overlay (where red nodes indicate they are upregulated) and the one on the right shows variant gain/loss data for the same genes where green equates to loss of function. In this example, although CHK1 is overexpressed in the dataset, it is predicted to have loss of function due to mutation.

Improve your RNA-Seq workflow with seamless upload of Cuffdiff data files.

Cuffdiff (part of the Cufflinks package) is one of the most popular software tools to quantitate differentially expressed genes or isoforms in RNA-Seq data. Now IPA makes it incredibly easy to upload datasets in Cuffdiff’s native “.diff” format.


Fig 4.Direct upload of Cuffdiff file. This shows a three-observation .diff file being uploaded to IPA. At this point you can save the file into an IPA project folder. The .diff file was obtained here as one of the supplementary files.