MetaPhOR

MetaPhOR assesses metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) to produce pathway-level scores and visualizations for KEGG pathways.

Key Features:

• DEG Input Compatibility: Accepts differentially expressed gene lists with fold change and p value from DESeq2 or limma, along with sample size.
• KEGG Pathway Scoring: Generates a data frame of scores for each KEGG pathway representing the magnitude and direction of transcriptional change, with estimated p-values.
• Visualization Methods: Produces bubble plots, heatmaps, and pathway models to display metabolic profiles within and between samples.

Scientific Applications:

• Metabolic Dysregulation Assessment: Evaluates transcriptional changes in metabolic pathways from RNA-sequencing or Microarray data.
• Metabolic Profile Comparison: Visualizes and compares metabolic profiles across samples or conditions using KEGG pathway-based scores.

Methodology:

MetaPhOR processes differentially expressed gene lists from DESeq2 or limma to calculate scores for KEGG pathways, then visualizes results through bubble plots, heatmaps, and pathway models.