Biomarker Identification-Sample Classification SCUDO

BI-SCUDO (biomarker identification-sample classification SCUDO) is a normalization-free, rank-based tool to classify expression profiles, typically for diagnostic/prognostic purposes. Given a set of expression profiles, one per subject, the tool works by first extracting a rank-based signature given by the identifiers of the n1 most expressed probes and the n2 least expressed probes. Subject signatures are then compared by means of a distance measure based on the definition of weighted enrichment score to obtain a signature distance matrix, which is then used to infer a classification of the profiles according to a phenotype of interest (such as control/disease status). Classification results are then displayed by a new graphical formalism that produces an unambiguous and easy to read sample-to-group assignment chart. Statistics and p-values are automatically computed to assess the quality of the output and to enable comparisons with other methods. Results include also a biomarker panel which clearly identifies the list of gene/miRNA/protein levels that BI-SCUDO uses to compute sample classification.

BI-SCUDO, COSBI, The Microsoft Research - University of Trento Centre for Computational and Systems Biology,

Lauria M. Rank-based transcriptional signatures: a novel approach to diagnostic biomarker definition and analysis, Systems Biomedicine 1(4):35-46, 2013.

Lauria M., Moyseos P., Priami C. SCUDO: a tool for signature-based clustering of expression profiles, Nucleic acids research 43 (W1), W188-W192, 2015.

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Lacroix S. et al. Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes, Genes & Nutrition 10(6):1-10, 2016.


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