The new look of this IPA release includes a redesigned Quick Start window and highly informative short videos to help orient you with quick overviews of IPA’s key features. The new look brings sharper graphics, new iconography and crisper fonts to IPA.
The new look for IPA. Almost all of the functionality of the new version is the same as the prior version, but now has a new appearance.
Please note that Mac users must switch to using the native command key modifier for Mac OS when using IPA. For example, to select all nodes in a network, press ⌘-A on the keyboard for Mac (instead of control-A, used for Windows).
Although any recent IPA installer is compatible with this release, we recommend downloading the latest IPA installer to obtain the new app icon: https://analysis.ingenuity.com/pa/installer/select. Note that IPA requires Java 8 or higher (which is built into this installer) to launch.
The IPA Quick Start window has been reimagined to provide helpful explanations and links so that you can use IPA more effectively right away. You will find sections on how to analyze various data types, links to the top help articles, new case studies, shortcuts to the main functions in IPA, how to contact Support and more.
The new Quick Start window. Headers at the left of the Quick Start give you an overview of available content: click the header to view the content. To open this window, go to Help > Quick Start or press control-9 on your keyboard for Windows or ⌘-9 for Mac).
New short videos can be accessed from the Core Analysis tabs. To view a video, click the video play button icon , which appears in the right corner of most tabs. As an example, here is a video for Upstream Regulators in IPA. A new overview video is also available for the My Pathway window.
The new IPA Graphical Summary provides you with a quick overview of the major biological themes in your IPA Core Analysis and illustrates how these concepts relate to one another. This feature selects and connects a subset of the most significant entities predicted in the analysis, creating a coherent and comprehensible synopsis of the analysis. The Graphical Summary can include entities such as canonical pathways, upstream regulators, diseases and biological functions. The algorithm constructs the summary using machine learning techniques to prioritize and connect entities and infers relationships to connect entities not yet connected by findings in the QIAGEN Knowledge Graph. These inferred relationships help you visualize related biological activities.
The Graphical Summary tab is available in the Core Analysis window. The example below shows the Graphical Summary result for an expression analysis of aggressive “claudin-low” breast cancer cell lines compared (i.e., ratio’ed) to less aggressive luminal A type breast cancer cell lines. In this dataset, which is based on PMID 20813035, the epithelial-mesenchymal transition (EMT) in claudin-low cells has been activated by specific transcription factors, such as ZEB1, SNAI1 and SNAI2, and the cells exhibit tissue-invasive tendencies — all of which are well represented in the generated summary:
The new Graphical Summary presents a synopsis of the top results from your Core Analysis as a small network. The algorithm for this feature uses a number of methods, including machine learning, to select and connect the top predicted entities. Analyses run prior to this release will take a little longer to open the first time they are viewed as IPA generates and saves the network presented in the Graphical Summary.
The summary takes a number of factors into account and is described in more detail in this help article. If you wish, you can generate a new summary with more or fewer nodes, and these changes will be saved automatically with your analysis.
This release enables you to add any number of “sticky” notes to a network or pathway to help you capture ideas or details of interest. Simply add notes to a pathway or network and save as a “My Pathway”. This tool is helpful for explaining the components of a custom pathway to others.
Communicate more effectively by adding your own notes to pathways and networks. Make notes for yourself or to share with others. You can attach notes to individual molecules and relationships or to provide general information about the pathway. Save the annotated pathway or share with your colleagues.
Four new Canonical Signaling Pathways
Addition of Activity Patterns to two existing Canonical Signaling Pathways
Approximately 425,000 new findings (bringing the total in IPA to over 7.6 million)
OmicSoft analysis content in Analysis Match and Activity Plot. More than 7,700 new analyses have been added in this release.