iPathwayGuide Release Notes
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 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.
– 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.
– 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.
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.
- iVariantGuide: API Client now accepts multi-sample analyses
- Improvements to account registration page to ensure proper organization affiliation.
- iPathwayGuide: Improvements to parsing of CuffDiff-formatted files to maintain association of phenotype labels. Fold changes and p-value parsing remains untouched.
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|
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)
- 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