micrographite

micrographite performs topological pathway analysis by integrating gene and miRNA expression profiles with validated and predicted miRNA-target interactions to incorporate post-transcriptional regulation into pathway analyses and is implemented as an R package.

Key Features:

• Integration of Gene and miRNA Expression Profiles: Combines gene and miRNA expression data to represent both coding and non-coding regulatory relationships.
• Utilization of Validated and Predicted Interactions: Incorporates experimentally validated and computationally predicted miRNA-target interactions into pathway analyses.
• Topological Pathway Analysis: Accounts for network topology to identify regulatory circuits and subpathways within biological pathways.
• Pathway Representation in Formal Maps: Enables inclusion of miRNAs into formal pathway maps such as KEGG and Reactome to enrich post-transcriptional regulatory information.

Scientific Applications:

• Study of Complex Diseases: Applied to investigate diseases where gene and miRNA regulation play a pivotal role.
• Epithelial Ovarian Cancer Transcriptome Analysis: Used to dissect the epithelial ovarian cancer transcriptome and define regulatory circuits specific to ovarian cancer histotypes.
• Personalized Medicine Research: Supports discovery of disease-specific regulatory circuits that can inform personalized medicine approaches.

Methodology:

The methodology builds upon updated versions of the graphite and CliPPER Bioconductor packages and integrates these with miRNA-target interaction data.