pcxn

PCxN (Pathway Coexpression Network) is a software tool that provides a comprehensive approach to understanding the relationships between biological processes. Pathways are groups of genes that work together to carry out specific functions and are essential components of biological processes. However, the complex interactions between pathways are not yet fully understood, and limited functional references for global pathway relationships exist.

PCxN solves this problem by quantifying the coexpression between more than 1,300 canonical pathways from the Molecular Signatures Database (MSigDB). This tool establishes a unifying interpretation of functional interaction between pathways by estimating the correlation between valid pathways in a broad context. The correlation estimation is based on a curated collection of 3,207 microarrays from 72 normal human tissues.

One of the unique features of PCxN is that it accounts for shared genes between annotations to estimate significant correlations between pathways with related functions rather than with similar annotations. This approach provides a more accurate and comprehensive understanding of pathway relationships.

Using PCxN, researchers can gain novel insights into the mechanisms of complex diseases. An Alzheimer's Disease case study demonstrated that PCxN retrieved pathways significantly correlated with an expert-curated AD gene list. These pathways have known associations with AD and were significantly enriched for genes independently associated with AD. PCxN complements gene set enrichment method results by revealing relationships between enriched pathways and identifying additional highly correlated pathways.