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We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes. ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two lists of genes and comprehensively visualizes(More)
The role of the adaptive immune response in controlling the growth and recurrence of human tumors has been controversial. We characterized the tumor-infiltrating immune cells in large cohorts of human colorectal cancers by gene expression profiling and in situ immunohistochemical staining. Collectively, the immunological data (the type, density, and(More)
Follicular Lymphomas (FL) and diffuse large B cell lymphomas (DLBCL) must evolve some immune escape strategy to develop from lymphoid organs, but their immune evasion pathways remain poorly characterized. We investigated this issue by transcriptome data mining and immunohistochemistry (IHC) of FL and DLBCL lymphoma biopsies. A set of genes involved in(More)
Cancer cells co-cultured in vitro reveal unexpected differential growth rates that classical exponential growth models cannot account for. Two non-interacting cell lines were grown in the same culture, and counts of each species were recorded at periodic times. The relative growth of population ratios was found to depend on the initial proportion, in(More)
We have previously defined the immune contexture as the type, density, location and functional orientation of tumour infiltrating immune cells, associated with patient prognosis in colorectal cancer (CRC). Here we describe potential mechanisms, including the DNA damage response (DDR) and cellular senescence, as contributing factors in shaping this(More)
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