In this release, several features in IPA have been improved for ease of use. An important aspect of IPA is the ability to overlay and visualize data on a network or pathway. Now, you can simultaneously see more rows in the ‘Matching molecules’ table and more easily display node bar charts on a network or pathway.
In the ‘Matching molecules’ table in ‘Overlay’ > ‘Analyses, Datasets, & Lists’, the default view now shows only the overlaid expression or phosphorylation measurement type (such as ‘fold change’) rather than all the available measurement types in the dataset. This modification enables you to view more rows of the table and is especially useful when the dataset has several measurement types (such as ‘p-value’, ‘FDR’ and ‘Intensity’). Additionally, when you add a second analysis or dataset, the small bar charts (node charts) now appear next to the nodes in the network or pathway by default (see Figure 1).
Figure 1: Streamlined overlay of ‘Analyses, Datasets, & Lists’ content. The defaults and controls for data overlay have been changed to simplify your work, allowing you to view more rows at once by default. Now, only the measurement that is overlaid on the network or pathway (such as ‘log ratio’ or ‘fold change’) is shown in the ‘Matching molecules’ table at the left. You can click the gear icon to add more measurement types for display. In addition, by default, node bar charts will appear automatically on the network or pathway at the right when multiple analyses or datasets are overlaid. In prior releases, you had to first select one or more rows in the ‘Matching molecules’ table to show the bar charts in the network.
Another improvement in this release allows you to visualize a miRNA–mRNA network directly from ‘microRNA Target Filter’ with one click. Select one or more rows in the dataset and click the new ‘Display as Network’ button (see Figure 2) to create a ‘My Pathway’, which automatically shows the miRNAs connected to their targets.
Figure 2: New ‘Display as Network’ button in ‘microRNA Target Filter’. Visualize rows in ‘microRNA Target Filter’ as a network by selecting one or more rows and clicking the ‘Display as Network’ button. The miRNAs are connected to their targets with miT and E edges (miRNA targeting and expression, respectively).
To ensure consistent network visualization in IPA, the ‘Display as Network’ button is also available in the ‘Causal Networks’ and ‘Regulator Effects’ tabs in ‘Core Analyses’.
Search and filtering of ‘Analysis Match’ analyses enhanced with added metadata
Now there are more ways to find and filter relevant analyses: ‘PubMed ID’ and ‘Therapeutic Area’ fields have been added to QIAGEN OmicSoft datasets and analyses. In Figure 3, a PubMed ID (PMID) is used in the ‘Dataset and Analysis Search’.
Figure 3: Searching for OmicSoft datasets using PMIDs. Enter only the integer portion of the PMID to search, as shown.
You can also search the OmicSoft ‘Therapeutic Area’ metadata with many keywords, such as neurology, rheumatology or endocrinology.
Three new Canonical Signaling Pathways
Addition of Activity Patterns to three existing Canonical Signaling Pathways
>104,000 new findings (bringing the total in IPA to over 7.7 million), including the following:
~24,000 expert findings
~44,000 cancer-mutation findings from ClinVar
~18,000 proteinâ€“protein-interaction findings from BioGRID
~2,300 Gene Ontology findings
~750 drug-to-disease findings from ClinicalTrials.gov
~600 target-to-disease findings from ClinicalTrials.gov
~31,000 proteinâ€“protein-interaction findings from IntAct
~500 newly mappable chemicals
>6900 new datasets for a total of >80,000 in Analysis Match and Activity Plot
Table 1: OmicSoft analysis content in ‘Analysis Match’ and ‘Activity Plot’. More than 6900 new analyses have been added in this release.