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Roberto Puzone performed the microarray dataset analysis and participated in the interpretation.
A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which cannot be detected by means of individual gene expression techniques using raw or corrected p values (FDR).
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See also Electronic supplementary material (ESM) methods for heatmap and public microarray datasets analysis.
Despite the need of an experimental validation of these new biological hypotheses, one of our goals was to exemplify and stress the importance of public microarray datasets analysis by using different and novel bioinformatics models and thus expand knowledge and information about important biological problems.
Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways.
KC carried out the selection of microarray datasets, biclustering analysis, functional analysis, and drafted the manuscript.
In the present study, we used a combination of hierarchical clustering and overall survival analysis of a novel microarray dataset, meta-analysis of published gene profiling studies, and cell culture experiments to investigate a potential role of a Notch-1 survivin Notch-1 survivinn breasignaling.
For the microarray meta-dataset analysis, all Affymetrix CEL files were downloaded from NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) for the U133 plus 2.0 array platform from published datasets.
First, we used a microarray dataset obtained from the analysis of several human wild-type and cancer tissues [ 12].
First, a microarray dataset was subjected to analysis using very stringent statistical criteria to define spleen leukocyte genes whose expression was different between the two strains of mice.
We further extracted the expression profiles of both mRNAs and the corresponding miRNAs from the microarray dataset GSE35982 for regression analysis.
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