FunHoP

FunHoP integrates RNA-seq data into KEGG pathway networks in Cytoscape by representing all functionally homologous proteins per reaction node and computing node-level expression values for differential pathway analysis.

Key Features:

• Comprehensive Gene Representation: Presents all genes associated with each enzymatic reaction node rather than only the first-listed gene as in some KGML readers such as KEGGScape.
• Integration of RNA-seq Data: Collapses multiple genes within a single network node into one representative measurement using RNA-seq read counts.
• Expression Value Calculation: Computes node expression values by accounting for read counts, gene length, and ratio to derive a single representative expression per node.
• Node-Level Differential Expression Analysis: Performs differential expression analysis at the network node level to assess pathway activity changes across conditions.
• Disease-Focused Demonstration: Has been applied to prostate cancer cohorts to identify consistent and biologically interpretable metabolic pathways.

Scientific Applications:

• Pathway analysis in metabolic networks: Enables more complete representation and analysis of metabolic pathways by including all functionally homologous proteins per reaction.
• Comparative condition analysis: Supports detection of pathway-level changes across experimental conditions or disease states using node-level differential expression.
• Disease mechanism investigation: Facilitates identification of pathways relevant to disease mechanisms, exemplified by analyses in prostate cancer cohorts.
• Target and biomarker discovery: Aids in prioritizing potential therapeutic targets and biomarkers by integrating expression data with pathway context.

Methodology:

KEGG data are loaded into Cytoscape via a KGML reader; FunHoP integrates RNA-seq read counts and collapses multiple genes per node into a representative expression value computed from read counts adjusted for gene length and ratio, enabling node-level differential expression analysis.