Pathway Volcano

Pathway Volcano filters and visualizes differential expression data by specific pathways to enhance biological interpretation and facilitate the identification of pathway-related changes.

Key Features:

• Pathway-Guided Filtering: The tool utilizes the Reactome API to select specific pathways and filter volcano plots to show only data associated with those pathways.
• Interactive Visualization: It provides interactive features to interrogate differential expression data through pathway-focused volcano plots.
• Data Export: The tool enables download of png files and tables containing pathway-associated data.

Scientific Applications:

• RNA-Sequencing Data Analysis: Pathway Volcano visualizes differential expression datasets from RNA-sequencing to reveal significant features within specified pathways that may be crowded in standard volcano plots.
• Proteomics Data Analysis: The tool supports visualization and interpretation of proteomics differential expression datasets through pathway-guided filtering.
• Biological Interpretation of Omics Data: It simplifies the interpretation of large and complex omics datasets by focusing on biologically relevant pathways rather than individual features alone.

Methodology:

The tool was developed as an R Shiny application in R version 4.3.3 using R Studio. It utilizes the Reactome API for pathway selection and requires the packages ggplot2, plotly, shiny, dplyr, and ReactomeContentServer. Volcano plots display log2 transformed fold change on the x-axis and negative log10 of a P-value on the y-axis, with filtering applied to show only pathway-associated features.