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