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Nuno Saraiva-Agostinho, Bernardo P de Almeida, Nuno L Barbosa-Morais (Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal; Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria)
The Connectivity Map (CMap) is a repository of thousands of genetic and pharmacological perturbations in human cells. Comparing differential gene expression profiles with those from CMap allows to infer molecular causes for the observed differences, as well as compounds that may promote or revert those changes. This can be done using user-friendly tools from clue.io. However, clue.io is difficult to automate for downstream analysis and does not support using local resources. We thus developed cTRAP, an R package to identify candidate causal molecular perturbations by comparing user-provided differential gene expression results with those from CMap using correlation and gene set enrichment score. cTRAP can also compare against gene expression/drug sensitivity associations derived from the NCI-60, the Cancer Therapeutics Response Portal and the Genomics of Drug Sensitivity in Cancer, to identify compounds that may target the phenotypes associated with the user-provided differential expression profiles. cTRAP is available in Bioconductor (bioconductor.org/packages/cTRAP). We are currently developing an easy-to-use visual interface to guide users through cTRAP’s analyses.