MINT – a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms

Molecular signatures identified from high-throughput transcriptomic studies often have poor reliability and fail to reproduce across studies. One solution is to combine independent studies into a single integrative analysis, additionally increasing sample size. However, the different protocols and technological platforms across transcriptomic studies produce unwanted systematic variation that strongly confounds the integrative analysis results. When studies aim to discriminate an outcome of interest, the common approach is a sequential two-step procedure; unwanted systematic variation removal techniques are applied prior to classification methods.

To limit the risk of overfitting and over-optimistic results of a two-step procedure, University of Queensland researchers developed a novel multivariate integration method, MINT, that simultaneously accounts for unwanted systematic variation and identifies predictive gene signatures with greater reproducibility and accuracy. In two biological examples on the classification of three human cell types and four subtypes of breast cancer, the researchers combined high-dimensional microarray and RNA-seq data sets and MINT identified highly reproducible and relevant gene signatures predictive of a given phenotype. MINT led to superior classification and prediction accuracy compared to the existing sequential two-step procedures.

MINT study-specific sample plots showing the projection of samples

rna-seq

a METABRIC Discovery, b METABRIC Validation and c TCGA-RNA-seq experiments, in the same subspace spanned by the first two MINT components. The same subspace is also used to plot the (d) overall (integrated) data. e Balanced Error Rate and classification accuracy for each study and breast cancer subtype from the MINT analysis

Availability – MINT is computationally fast as part of the mixOmics R CRAN package, available at http://www.mixOmics.org/mixMINT/ and http://cran.r-project.org/web/packages/mixOmics/

Rohart F, Eslami A, Matigian N, Bougeard S, Lê Cao KA. (2017) MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. BMC Bioinformatics 18(1):128. [article]

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