iPathwayGuide Release Notes
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
On June 21, 2019, Advaita released a major update to its platform, with improvements to iPathwayGuide, iVariantGuide, and iBioGuide.
IMPROVEMENTS
The Advaita Knowledgebase was updated to version 1906 and now includes:
- 3 organisms: homo sapiens, mus musculus, rattus norvegicus
- 216,544 Genes
- 2,307 Diseases
- 45,049 GO terms
- 5,694 Drugs
- 985 Pathways
- 5,396 miRNAs
- 92,745 Proteins
- 29,761,157 References
- 3,042,479 Interactions
- 477,289 Experiments
For a complete list of databases and versions, please see report information within each application.
NEW FEATURES
- iBioGuide: Users can now log in to iBioGuide using their Advaita credentials, the same account they use for iPathwayGuide and iVariantGuide.
- iPathwayGuide: Experiment and references for Network Analysis are now shown in a paged view, improving load time.
BUG FIXES
- iPathwayGuide: Meta-Analysis icon was updated to stay consistent with menu selections.
On March 16, 2019, Advaita released a major update to its platform, with several major improvements to iPathwayGuide. As with all major releases, new features are available in all analyses generated after the update was released. To see new analysis modules with older analyses, please update the analysis using the button found in report information, “Re-run as new analysis.”
NEW FEATURES
– NEW MODULE: Predicted Upstream Regulator Analysis allows you to find genes that have regulatory interactions consistent with expression patterns in DE genes. Several parts of the application were updated to include the new analysis module, including: Printable Report, Meta-Analysis, API, toolbar, and more.
MAJOR IMPROVEMENTS
– DE down-regulated genes are now shown as blue in the volcano plot, corresponding with the coloring used in gene bar plots, on pathways, and in networks.
– Genes data export now includes option to export all genes as TSV file— convenient for uploading to iPathwayGuide as a new analysis.
– Pathway data export now includes p-values for pORA and pAcc in addition to the combined p-value, pComb.
– Updated text of the printer-friendly report that is auto-generated with every analysis.
– Improvements to registration flow and application selection page
– Updated layout for the table of annotation sources inside the report info section. The new layout accommodates sources for Network Analysis and Predicted Upstream Regulator Analysis.
BUG FIXES
– Registration page layout is fixed for the newest version of Chrome browsers
– Tooltips are now more responsive and more visible in iPathwayGuide
– Fixed a bug in network analysis causing long GO terms to spill out of their boxes
– Fixed a bug affecting the navigation bar display on smaller screens
On January 12, 2018, Advaita released a major update to its platform, with improvements to iPathwayGuide, iVariantGuide, and iBioguide.
IMPROVEMENTS
The Advaita Knowledgebase was updated to version 1711 and now includes:
- 3 organisms: homo sapiens, mus musculus, rattus norvegicus
- 213,390 Genes
- 1,933 Diseases
- 44,976 GO terms
- 4,791 Drugs
- 955 Pathways
- 5,710 miRNAs
- 3,161,730 References
- For a complete list of databases and versions, please see report information within each application.
NEW FEATURES
- iVariantGuide: API Client now accepts multi-sample analyses
- Improvements to account registration page to ensure proper organization affiliation.
BUG FIXES
- iPathwayGuide: Improvements to parsing of CuffDiff-formatted files to maintain association of phenotype labels. Fold changes and p-value parsing remains untouched.
3/13/2017
With Advaita’s latest update to its applications and knowledge base, Advaita updated its API for iVariantGuide and iPathwayGuide.
An API or (Application Program Interface) is a set of routines, protocols, and tools for building software applications. An API specifies how software components should interact. Advaita’s API is designed.
On February 27, 2017, Advaita released a major updates to its platform. These are the release notes.
IMPROVEMENTS TO: iPathwayGuide, iVariantGuide, iBioguide, and the Advaita Knowledge Base
- Changes to AWS services in preparation for HIPAA compliance
- Updated knowledge base to version Advaita KB v1702, which includes the following data sources and versions:
| Database | Version | iPG Annotations | iVG Annotations |
|---|---|---|---|
| KEGG | Release 81.0+/01-20, Jan 17 | Pathways, Diseases, Drugs | Pathways |
| Gene Ontology | 2016-Sep26 | GO Terms | GO Terms |
| Targetscan | Targetscan v7.1 | miRNA Target Genes | miRNA Target Genes |
| MIRBASE | MIRBASE v21,06/14 | miRNA Sequences | |
| dbSNP (incl 1k genomes) | Build 149 | Minor Allele freq. | |
| RefSeq | Release 71 July 2016 | Impacted Transcripts | |
| ClinVar | Dec 1, 2016 | Clinical Significance | |
| SNPEff | v4.1L | Predicted Impact |
IMPROVEMENTS TO iPATHWAYGUIDE
- NEW FEATURE! Onboarding carousel with top user benefits
- NEW FEATURE! API (Premium feature)
- Bug fix: genes selected in Genes Table on Pathways page are now highlighted on pathway map
IMPROVEMENTS TO iVARIANTGUIDE
- Improved error messaging for sample upload & report creation
- NEW FEATURE! Versioning: each report now shows which version of the Advaita Knowledgebase was used to annotate the sample. Outdated reports may be updated when viewing Report Info: either on the Reports page or from within the report itself. As is true for other Advaita applications, only the report owner may update it.
IMPROVEMENTS TO iBIOGUIDE
- Updated to use AKB v1702
The following components were added or addressed in this release.
- Extensive databases updates including:
- KEGG pathways, drugs, and diseases
- NCBI genes
- TargetScan miRNAs
- Gene Ontologies
- PubMed references
- New EdgeR import format support
- Improvements to several of the exported images
- Improvements to meta analysis to preserve order of comparisons
- Several bug fixes
- Changes to support additional AWS features
- Enhancements to security
The following components were added:
- Support for Sciex SWATH 2.0 Proteomics Expression data
- “Trash” bin on user dashboard
- Pathway and ontology images are now locked for scrolling. They can be unlocked in the on-screen menu.
- In the pathway images, individual genes can now be selected if you hover over the node in the image.
- Coherent cascades now have arrow heads so you can see directionality of the cascade.
- The gene table in the pathway detail page is more refined. Easier to filter.
- Bar chart of DE genes for pathways is now presented below the pathway image.
- Meta-analysis has a new view called “Rank layout” that lets you see how genes, GO terms, pathways, etc, rank compared to each other. (accessible from the
- lower right corner of the Venn).
- Several other improvements on the back-end and a few bug fixes.
Knowledge Base Updates:
- Genes – 195,222 (increase of 23,106)
- Pathways – 871 (increase of 12)
- micro RNAs – 8,837 (increase of 5,268)
- GO Terms – 39,907 (increase of 1,880)
- Drugs – 4,389 (increase of 229)
- Diseases – 1,411 (increase of 12)
- SNPs – 92,169,423 (increase of 32,120,131)
- References – 3,010,588 (increase of 51,977)
New Features:
- Support for nSolver data from NanoString Technologies
- QC and Normalization metrics for Affymetrix CEL files
- Stem-loop information for miRNAs
- Printable report summary with detailed methods and references
- “Line-up” comparative ranking chart in meta analysis