On January 31, 2020, Advaita released a major update to its platform, with two brand new capabilities and three major improvements, now available in iPathwayGuide. As with all iPathwayGuide releases, many of the improvements are available in older analyses. Other features, including the two new capabilities, are only available in analyses generated after the update was released. To access these new capabilities for older analyses, please update the analysis using the button found in report information, “Re-run as new analysis.”
NEW CAPABILITIES: Available in newly created or updated analyses
New Module: Upstream Chemicals, Drugs, and Toxicants
Predicted Upstream Chemical Analysis allows you to predict chemicals, drugs, and toxicants that might be present (overly-abundant) or absent (insufficient) in your experiment. This analysis compares chemical-to-gene regulatory interactions with patterns of downstream gene expression to find chemicals with large numbers of consistent downstream DE genes. To support this analysis, the Advaita knowledgebase was expanded (to v1910) to include 170,997 chemicals and 774,553 chemical-to-gene regulatory interactions. This new analysis capability is available from the Printable Report, Meta-Analysis, and Network Analysis, and navigation bar, where it can be found under the heading Upstream Regulators, along with Upstream Genes and miRNAs.
New Visualization: Dendrograms
iPathwayGuide now offers dendrograms, as an additional way to visualize relationships across results. The dendrogram visualization groups together significant results (annotations) that have DE genes in common. This visualization is available for all GO terms, pathways, upstream regulatory genes, and chemicals. It is also available in Step 1 of the updated Network Analysis module, where it can be used to select the set of genes of interest based on annotations that have DE genes in common.
MAJOR IMPROVEMENTS: Available in existing analyses
New Analysis Workflow: Select genes of interest in Network Analysis
The Network Analysis page has been redesigned to allow users select genes of interest from the results of all analyses modules (biological processes, pathways, diseases, miRNAs, upstream regulators and more). Other improvements to the Network Analysis module include:
- the ability to add Chemicals to networks to visualize interactions with downstream genes
- the ability to save & reload networks
- the ability to export network images as .png and .svg
- and two new network layouts: Gatekeepers and Regulators
- new onboarding tutorial and videos
Note: these capabilities are available in analyses generated or updated after October 2018.
New Analysis Workflow: The Intake Page now displays file parsing warnings. This allows you to preview which lines from your input file were ignored, and for what reason.
New Feature: Results from any module may be searched by associated genes, e.g. find significant pathways containing BRCA1