SIM

SIM (Set Integration Model) is a software tool that jointly analyzes DNA copy numbers and RNA expression data from microarray experiments. The tool uses a gene set-based approach to robustly and sensitively detect associations between gene dosage and gene expression levels rather than focusing on individual genes. SIM is advantageous for identifying associations with long-spanning, low-amplitude copy number aberrations. The model allows for additional explanatory variables and does not require a mapping between copy number and expression probes. By integrating multiple microarray datasets, SIM enables the prioritization of putative targets for functional validation, making it a powerful tool for understanding the role of genes in tumorigenesis.