GeMoNe (the GEnomic of MyelOid NEoplasms) is a data portal that integrates, collects and analyzes heterogeneous molecular data (e.g. somatic mutations and gene expression) coming from high-throughput experiments performed on biological samples of different Myeloid Neoplasms.
M.Cazzola, Haematologica, 2010
M.Gerstung, Nature, 2015
Data are modeled on two main concepts: Sample Cohorts and Genomic Signatures. Once defined, the user can freely combine them by one of the available analytical tools (e.g. Kaplan-Meier survival analysis).
Each sample in the database belongs to a specific project (e.g. TCGA). User creates a
cohort by pooling samples together. Filters allow to select samples basing on disease, project,
age, ethnicity etc.
Note: for each sample, a certain set (and type) of genomic data is available. Users should be aware on how to correctly combine samples (especially those from different projects) in order to obtain meaningful results.
A genomic signature consists in one or more genomic region of interests (e.g. Genes and Pathways), characterized by one or more molecular data type (e.g. somatic mutations and mRNA expression).
Kaplan-Meier Survival Analysis
Given a genomic signature, a cohort is divided in two groups: samples with at least one genomic event and those with no genomic events within the signature. An event can be a somatic mutation, an up-regulated mRNA or a particular CNV. Users can thus compare survival curves of different sample groups (or eventually the same) , characterized by a particular genomic signature consisting of heterogeneus molecular data.
M.G. Della Porta, Leukemia, 2015