LSTrAP-Lite

LSTrAP-Lite constructs gene co-expression networks from RNA sequencing data to identify enzymes and transcription factors involved in biosynthetic pathways.

Key Features:

• Affordable Computing: Operates on low-cost, compact hardware to allow analyses on resource-limited systems.
• Quality Control and Data Handling: Includes modules for downloading RNA sequencing datasets and performing quality control to select high-quality data for downstream analyses.
• Gene Co-expression Network Generation: Constructs gene co-expression networks from processed RNA sequencing data to reveal gene–gene relationships.
• Biosynthetic Pathway Analysis: Applies network analyses to dissect biosynthetic pathways, demonstrated on artemisinin biosynthesis in Artemisia annua.
• Transcription Factor Identification: Analyzes co-expression networks to suggest candidate transcription factors regulating biosynthetic processes.

Scientific Applications:

• Plant biology: Investigating the genetic basis of secondary metabolite production and gene expression across plant species.
• Pharmacognosy: Informing discovery and characterization of plant-derived pharmaceuticals such as artemisinin.
• Gene function and regulatory network prediction: Predicting gene function and regulatory networks from publicly available RNA sequencing data.

Methodology:

Computational steps include automated downloading of RNA sequencing datasets, implementation of quality control measures, generation of gene co-expression networks, and application of network-based pathway analysis.