transcriptogramer

transcriptogramer performs systems-level differential expression analysis by projecting gene expression onto an ordered gene list derived from protein–protein interaction (PPI) network topology to detect coordinated perturbations across functionally associated genes.

Key Features:

• R/Bioconductor implementation: Implemented as an R/Bioconductor package for integration with R-based transcriptomic workflows.
• PPI-based gene ordering: Derives an ordered list of genes from protein–protein interaction (PPI) network topology to encode functional relationships.
• Expression projection: Projects gene expression values onto the PPI-derived ordered gene list.
• Topological smoothing: Applies topological smoothing across the ordered gene list to incorporate neighborhood effects from the PPI network.
• Systems-level differential analysis: Performs differential expression analysis at the pathway/system scale to identify coordinated changes across gene groups.
• Gene ontology enrichment: Conducts gene ontology enrichment while accounting for functional relationships encoded in the interaction network.

Scientific Applications:

• Pathway and system perturbation detection: Identification of entire biological systems that are significantly perturbed in case–control transcriptome experiments.
• Detection of coordinated dysregulation: Revealing coordinated biological dysregulation among functionally associated genes that may be overlooked by gene-centric analyses.
• Functional annotation of perturbations: Interpreting system-level expression changes using gene ontology enrichment informed by PPI structure.

Methodology:

Project gene expression values onto an ordered gene list derived from PPI network topology, apply topological smoothing, perform differential expression analysis, and conduct gene ontology enrichment.