Advaita iPathwayGuide

iPathwayGuide is a gene and protein expression analysis tools that use a systems biology approach to identify significantly impacted pathways, gene ontology terms, diseases, and predicted microRNAs based on the given gene or protein differential expression signature. iPathwayGuide uses the most advanced pathway analysis approach that considers the role, positioning, and relationships of a given gene within a pathway, resulting in a significant reduction in false positives associated with pathway analysis.

Perform next-gen pathway analysis using Advaita’s proprietary “Impact Analysis” method to identify significant pathways without the noise found in other approaches. Simple, easy, web-based application.

Input formats supported

  • CuffDiff
  • DESeq
  • EdgeR
  • JMP Genomics
  • nSolver (NanoString Technologies)
  • Generic tab delimited .txt file (must contain gene symbol, log2FC, p-value)
  • SCIEX SWATH 2.0 proteomics data files
  • Select Affymetrix CEL files

Gene Analysis

  • Accepts the entire list of genes, associated fold changes, and p-values to quickly select for significant differential expression (DEGs)
  • Identify individual genes and learn about annotated miRNAs, ontologies, pathways, SNPs, drugs and diseases

Pathway Analysis

  • Uses “Impact Analysis” which assess significance using two forms of evidence (enrichment and perturbation)
  • Considers type, function, and interactions between each gene
  • Map DEGs directly on a pathway
  • Model drugs, miRNAs, and SNVs directly on pathways to form plausible hypotheses

Gene Ontology (GO) Analysis

GO analysis for the three domains:

  • Biological Processes
  • Molecular Functions
  • Cellular components
  • Offers advanced correction factors including Elim and Weight pruning methods that take hierarchical relationships into consideration and provide more meaningful results
  • Identify and explore annotated genes, and view hierarchy plots of the various GO terms.

miRNA Prediction

  • Predict micro RNA (miRNA) activity based on gene-expression or protein-expression signatures
  • Identify miRNAs that may be active in the phenotype
  • Identify targets and generate new hypotheses

Disease Analysis

  • Highlights enriched diseases under the ICD-10 classification
  • Quickly zoom in on groups of diseases and see significantly expressed genes from your data annotated to each disease
  • Choose from a variety of correction factors including FDR
  • Identify and explore annotated genes, references, and more.


  • Compare and contrast changes across multiple conditions
  • Quickly identify genes, pathways, micro RNAs, GO terms, or diseases that may be in common or unique across your data
  • Visualize changes in expression at each gene across conditions or pathways
  • Rank relevant pathways, GO terms, miRNA based on conditions
  • Build custom meta-analyses based on other datasets you may already have or public data

Exporting and Sharing

  • Each data set comes with a printable summary including methods, results, and references
  • All images are exportable in both .png and .svg format
  • All tables are exportable as .csv files
  • Share the entire analysis with any colleague inside or outside NCI by typing in the recipient’s email (receiver does not need a license, but does need a free account)

Just-in-time Education and Support

  • 1-2 minute embedded videos provide relevant instruction on the page you are looking at
  • Extensive webinars and other support resources available 24/7
  • Unlimited phone and email support

Access Information

You must submit a request through “NCI at Your Service” to obtain the access code before visiting the Advaita Bioinformatics website to register for access.

iPathwayGuide is available to all researchers affiliated with the NCI. Once you have obtained the access code, please use the registration link below to initiate your user account (NCI affiliated e-mail address required).

Registration link: New Account Registration