WoPPER

WoPPER analyzes position-related gene expression in prokaryotes to identify chromosomal regions with coordinated differential expression by integrating RNA-sequencing or microarray data with genomic annotations.

Key Features:

• Integration of Gene Expression Data: Accepts RNA-sequencing or microarray gene expression data as input for analysis.
• Genomic Annotation Utilization: Uses an internal database of annotations for 2780 bacterial strains or accepts custom genomic annotations.
• Identification of Differentially Expressed Regions: Detects clusters of positionally related genes exhibiting coordinated trends in differential expression.
• Graphical Representations: Produces graphical outputs including circular plots of analyzed chromosomes to visualize positional expression patterns.
• Methodological Foundation: Implements analysis procedures based on the R-package PREDA.

Scientific Applications:

• Regulatory Mechanism Discovery: Highlights chromosomal regions with coordinated differential expression to aid identification of potential transcriptional regulatory mechanisms.
• Spatial Genomics Studies: Enables investigation of the impact of genomic architecture and spatial organization of genes on transcriptional dynamics in bacteria.

Methodology:

Accepts RNA-sequencing or microarray expression data and genomic annotations (internal database of 2780 bacterial strains or user-provided), analyzes positionally related genes to identify clusters of coordinated differential expression, and implements the analysis using the R-package PREDA.