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Latest improvements for IPA

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What’s New in the IPA Fall Release (September 2021)

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Improve the presentation of your Canonical Pathway bar chart results

There are several new ways to customize your bar charts to make them easier to present and publish.

  • Tailor the bar chart to include or exclude pathways that contain a particular gene. Simply click the Customize Chart button and enter a gene of interest to limit the pathway bar chart to pathways that include that gene name. Or if desired, filter away all the pathways that contain a particular gene or set of genes. The genes you use to filter must be overlapping the pathway from your dataset. The pathways in the example below are filtered to display only those that contain the ETS1

Canonical pathways for a breast cancer dataset filtered to display only pathways containing the ETS1 gene.
 

  • Focus on pathway activity by sorting the bars or columns by z-score. The chart below has been sorted by z-score. As the y-axis scale for the chart remains -log(p-value), bar height is proportional to its right-tailed Fisher’s Exact Test significance; however, the bars are ordered on the x-axis from positive to negative z-score.

The unfiltered Canonical Pathway bar chart of the breast cancer pathways are arranged so that the pathways with the highest positive z-scores (predicted activation) are at the left .
 

  • Customize the font sizes in the chart for publication and presentation. You can increase the size of the font used in the bar chart, making the font larger for publications (compare the figure below with the figure above).

The figure above was modified to increase the font size of the bar and y-axis labels.

 

New IPA client installer: Please take action before December 2021

The client installer for IPA has been updated and now includes OpenJDK Java (version 11.0.2) instead of Oracle Java. The installer supports two-factor authentication (2FA), and all users will be required to use 2FA as of the December release of IPA.

The new installer will be required to launch the upcoming December release of IPA. Download the installer from  https://analysis.ingenuity.com/pa/installer/select. This page hosts installer packages for both Windows PCs and Macs. Note that a 32-bit version of OpenJDK is not available, so Windows users with a 32-bit operating system must instead download the Oracle Java version (also available from the link above). After downloading, install the new IPA client installer on your computer at your earliest convenience.

If you are unable to upgrade to the new installer for some reason, you can use Web Start with Oracle Java to launch IPA. Web Start cannot, however, be used with a Mac that has an M1 chip, as Oracle does not supply a version of Java Web start that is compatible with the M1 chip for Macs. Therefore, M1 Mac users must upgrade to the new installer to run the IPA December release.

Please contact Customer Support at ts-bioinformatics@qiagen.com if you experience any issues with the new installer.

 

Content updates

Six new Canonical Signaling Pathways

  • Neurovascular Coupling Signaling Pathway
  • Oxytocin Signaling Pathway
  • Pulmonary Fibrosis Idiopathic Signaling Pathway
  • Pulmonary Healing Signaling Pathway
  • Pyroptosis Signaling Pathway
  • Wound Healing Signaling Pathway

Activity pattern added and content updated for two pathways

  • G-Protein Coupled Receptor Signaling Pathway
  • Polyamine Regulation

Content updated for one pathway

  • Circadian Rhythm Signaling

>325,000 new findings (bringing the total in IPA to over 8.4 million), including the following:

~143,000 Expert findings

~66,600 protein–protein interaction findings from BioGRID

~400 protein–protein findings from IntAct

~12,000 findings from COSMIC

~86,350 cancer mutation findings from ClinVar

~12,000 findings from the Mouse Genome Database (MGD)

~1430 findings from the Online Mendelian Inheritance in Man (OMIM)

~1800 Gene Ontology findings

~1400 target-to-disease findings from ClinicalTrials.gov

~1800 drug-to-disease findings from ClinicalTrials.gov

~300 newly mappable chemicals

>6000 new datasets (for a total of >102,000) will soon be available in Analysis Match, Activity Plot and Pattern Search

Over 102,000 OmicSoft analyses are currently being computed on our servers and will be released when they have completed in the first week of October, 2021.

 

The more than 6000 additional analyses include a new Land repository called “Normal Cells and Tissues”. In this release, this Land contains 52 comparisons, based on RNA-seq data from the GTEx consortium, in which a set of samples from a single normal human tissue type is compared to a pool of samples taken from a large variety of other normal tissue samples.

IPA’s Graphical Summary of the “Brain – Hippocampus vs Others” comparison.

Normal tissue comparisons are useful for looking at tissue-specific markers and, for example, for matching with single-cell analyses.

“Brain – Hippocampus vs Others” analysis is matched against all single-cell data in IPA.

For Land Explorer users, the GTEx differential expression is available for each gene on IPA Gene Views.