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It must be emphasized that these differences were identified using an unsupervised analysis, i.e. without any prior information about the samples.
Biological network analysis was performed with Ingenuity Pathways Analysis IPAA) software using an unsupervised analysis.
Using an unsupervised analysis, we hierarchically clustered all time points from the cetuximab and gefitinib treatment experiments and identified over 500 genes that changed in expression at least 4-fold.
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In a pilot study of acute meningitis, CSF spectra from small numbers of controls, patients with viral meningitis and bacterial/fungal meningitis were distinguished using an unsupervised cluster analysis method [8], suggesting that classification according to etiology is possible using larger data sets.
This was confirmed using an unsupervised cluster analysis: the expression profiles at the same time points from different regions were similar to one another and therefore clustered together compared to those from neighboring time points (Additional file 1 figure S3).
Expression patterns of the five proteins were recognized using an unsupervised hierarchical cluster analysis.
Using an unsupervised hierarchical clustering analysis of genome-wide expression microarray data, the classical molecular classification divided breast cancers into five intrinsic subtypes: normal-like, luminal A, luminal B, HER2+ and basal-like subtypes [ 23].
The responses were compared across the cell types using an unsupervised agglomerative hierarchical clustering analysis (HCA) that classified the cells into separate branches of a cluster dendrogram.
Genes that passed filtering criteria were clustered into gene modules, based on their co-expression pattern, using an unsupervised "Weighted gene co-expression network analysis (WGCNA)" package in R 2.13 [ 23].
Using an unsupervised technique such as principal component analysis (PCA) and several supervised methods like classification and regression trees (CART), discriminant partial least squares regression (DPLS) and uninformative variable elimination DPLS (UVE-DPLS), we could confirm the uniqueness of sea biofilms and make a distinction between flowing water and standing water biofilms.
In this analysis we used an unsupervised multivariate analysis of NR activities and rodent liver lesions to investigate a potential mode of action for non-genotoxic hepatocarcinogenesis. Human NR activity for 309 environmental chemicals was obtained from in vitro high-throughput screening (HTS) experiments.
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