What’s New in the IPA Fall Release (September 2016)
Discover significant isoforms in RNA sequencing data with enhanced IsoProfiler
RNA sequencing technologies can generate datasets with thousands of differentially spliced transcripts. IsoProfiler helps you determine which isoforms have interesting biological properties relevant to your research project.
- Results are now expanded to include gene-level disease and function annotations to enable you to focus on potentially biologically interesting (but not yet well-understood) isoforms
- Quickly narrow down to the transcripts of interest by searching on specific gene names or disease or function terms
- Save time by visualizing isoform schematics inside IsoProfiler to understand the basic structure of the isoforms of interest
- Focus on protein-coding transcripts with the new transcript type column for RefSeq datasets
IsoProfiler is available in IPA with Advanced Analytics.
Visualize phosphoproteomics data on networks and pathways
Enhance your multi-omics research approaches by uploading simplified phosphoproteomics datasets to IPA for overlay onto networks and pathways. In a first step to better support the understanding of phosphorylation state and the associated biology, a new “phospho” measurement type is being introduced with this release of IPA. Overlay phosphorylation and expression profiles on networks and pathways to identify key areas where phosphorylation is impacting the biological activity of the encoded proteins.
If you have performed both gene expression and phosphoproteomics profiling, you can visualize both of these data types simultaneously as bar charts on networks and pathways. Figure 3 below shows the upstream regulator MAPK1 which IPA predicted to be activated by alpha-toxin (hemolysin) treatment of S9 cells. This prediction was based on a Core Analysis of the gene expression data after exposure to the toxin. The expression data shows that MAPK1 is not itself differentially expressed, but overlaying the accompanying phosphoproteomics dataset on the MAPK1 network provides a possible mechanism for its activation—MAPK1’s phosphorylation level is increased which is likely to activate it and lead to the observed expression changes downstream. In Figure 3, you can see in contrast that JUN is both upregulated and exhibits higher protein phosphorylation after the treatment.