Welcome to APA

Altered Pathway Analyzer via network connection rewiring

Altered Pathway Analyzer (APA) is a cross-platform and standalone tool for analyzing gene expression datasets to highlight significantly rewired pathways across case-vs-control conditions. The Tool is designed to analyze human gene expression datasets (with Entrez ID); however, the analysis can be performed on gene expression datasets of other species by using appropriate flags and input files. APA algorithm is unique prioritization algorithm that also uses gene-regulatory network to identify transcriptionally dysregulated pathways. It, thus, uses altered Transcription Factor (TF) and Target Gene (TG) relationship for prioritizing gene circuit rewired pathways. For Human datasets, it requires Gene expression matrices (RNAseq read count or Normalized gene expression values) with genes in Entrez ID format. For other species, please refer the manual


    → Predict rewired sub-network or dysregulated or altered pathways from gene expression datasets (RNAseq read count or normalized gene expression values).

    → Calculate TF-mediated differential regulation of each predicted pathway

    → Reveal rewired regulatory interactions, i.e. TFs and its TGs, in altered pathways.

    → Perform context-specific disease gene enrichment analysis.

    → Sub-network analysis for pathway-specific gene prioritization


RNAseq Read count matrices or Normalized gene expression profiles

Source Code

Download APA (Version 3.0) (File size: 4.5 MB).

Old release

APA has been tested only on linux machine but should also work on windows and Mac machines.

For more information about APA dependencies, its usage and input files format click here

Contact Information

Dr. Dinesh Gupta
Team leader, Translational Bioinformatics group
ICGEB, New Delhi, India

Abhinav kaushik