LSTrAP-Cloud

LSTrAP-Cloud generates gene co-expression and regulatory networks from large-scale RNA-seq transcriptome data to infer gene function and regulatory relationships.

Key Features:

• Data processing and quality control: Processes RNA-seq data and performs quality control to produce high-quality expression matrices.
• ENA input streaming: Streams RNA-seq data from the European Nucleotide Archive (ENA) as input for analysis.
• Gene co-expression network construction: Constructs gene co-expression networks to identify functionally related genes and modules.
• Regulatory network inference: Infers regulatory relationships among genes from co-expression patterns.
• Scalability for large datasets: Operates on large-scale transcriptome datasets derived from public RNA-seq resources.
• Cross-species compatibility: Applies to organisms with sequenced genomes and publicly available RNA-seq data, including non-plant organisms.
• Candidate gene identification: Shortlists candidate genes such as enzymes, transporters, and transcription factors for pathway and regulatory studies.

Scientific Applications:

• Gene function prediction: Uses co-expression and regulatory relationships to predict gene function and prioritize candidates for study.
• Pathway and regulatory analysis: Enables identification of genes involved in biosynthetic and transport pathways and their regulators.
• Nicotiana tabacum nicotine pathway case study: Identified enzymes, transporters, and transcription factors involved in nicotine synthesis, transport, and regulation in Nicotiana tabacum.
• Cross-species transcriptomic comparisons: Facilitates comparative analysis across diverse organisms with public RNA-seq data and sequenced genomes.
• Candidate selection for experimental validation: Produces ranked lists of genes for follow-up experimental validation or functional characterization.

Methodology:

Streams RNA-seq data from the European Nucleotide Archive (ENA), performs processing and quality control, and constructs gene co-expression networks to infer functional and regulatory relationships.