What’s New in the IPA Summer Release (June 2016)
Discover significant isoforms in your RNA sequencing data with the 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.
Identify isoforms with significant pattern(s) of expression, such as:
- Genes where isoforms are both upregulated and down regulated in the same dataset, which may have important functional consequences
- Isoform switching– when the most highly expressed (highest RPKM) isoform for a gene differs between the experiment and the control samples
- Multiple protein-coding isoforms expressed for the same gene
Prioritize the most significant isoforms by:
- The range of fold changes within each gene
- Highest differential expression
- Most or fewest transcripts per gene
Focus on important attributes of the isoforms:
- Isoforms that exceed thresholds that you set such as fold change, p-value, FDR, or RPKM
- Associated with known diseases or functions
- Encode proteins (as opposed to those with retained introns or are pseudogenes for example)
- Encode a principal isoform as annotated by APPRIS (http://bioinfo.cnio.es).
Visualize isoform-level expression in one dataset or across multiple datasets:
- Visualize isoforms with moderate fold changes that are highly abundant as compared to isoforms with large fold changes that are expressed at lower levels
- See which isoforms are similarly differentially expressed across multiple datasets
- Overlay transcript-level expression on a Network, Pathway or Isoform View
Drill-down into the “IsoProfiler Findings” view to explore the details about the isoforms that have disease or biological function findings captured from the literature. This is done by selecting rows (or all rows) in the top table and clicking the IsoProfiler Findings button at the top of the table. This will open a special window as shown in Figure 3. Only isoforms with disease or function associations will appear in this window. This table enables filtering on findings-level details using the funnels, or filters, above each column.
IsoProfiler is part of Advanced Analytics.