QPA

QPA performs quantitative pathway analysis to identify differentially expressed genes and pathways and to elucidate pathway-level mechanisms underlying the effects of traditional Chinese medicine recipes in heart failure.

Key Features:

• Optimized in silico analysis: Extracts gene expression information from sequencing and transcriptome data to identify differentially expressed genes and differentially expressed pathways (DEPs) across experimental groups.
• Pathway enrichment and PPI network studies: Performs pathway enrichment analysis and protein-protein interaction (PPI) network analysis to elucidate pharmacological mechanisms.
• Validation capabilities: Supports validation of heart failure (HF)–related genes predicted from DEP analysis using quantitative real-time PCR (qRT-PCR) and western blot.

Scientific Applications:

• TCM recipe mechanism dissection: Analyzes effects of Qishen granules decomposed recipes—Qingre Jiedu (QJ), Wenyang Yiqi (WYYQ), and Huo Xue (HX)—on molecular pathways relevant to heart failure.
• Experimental model analysis: Identifies HF-related genes and signaling pathways from gene expression data generated from heart failure Sprague-Dawley rats.
• Inflammatory and profibrotic signaling: Detects decreased expression of Spp1 and Cx3cr1 associated with reduced inflammatory and profibrotic signaling following QJ, WYYQ, and HX treatments.
• Oxidative stress and energy supply: Identifies decreased Myc and increased Adcy1 expression implicating reduced oxidative stress and activation of the cAMP–PKA signaling cascade linked to enhanced myocardial energy supply.
• Ventricular remodeling: Links attenuation of profibrotic signaling through Fgfr2 to mitigation of ventricular remodeling.

Methodology:

Performs sequencing and transcriptome analyses using in silico approaches to identify differentially expressed genes and integrates these results with pathway enrichment analyses and protein-protein interaction network studies.