For comparisons of molecular subtype classifications, we applied a commonly used classifier designed for single sample predictions, the 50-gene subtype classifier (PAM50) developed by Parker et al. [ 18].
Using the metagenomic approach and the VP6-based molecular classification scheme, we found evidence for a novel rotavirus species that we tentatively called Rotavirus I.
As a molecular classification tool, we used PFGE to genetically discriminate representative STEC O157 isolates.
To further improve the molecular classification of medulloblastoma, we have studied a series of 62 medulloblastomas at the mRNA expression level by Affymetrix HG-U133 plus2.0 GeneChips and characterized genomic abnormalities in a sub-set of these (n = 52) by comparative genomic hybridization (CGH) analysis using 30 K oligonucleotide arrays.
Using the gene expression profiles of robust molecular classifications of HCC published by Hoshida and colleagues, we determined the initial differentially expressed genes [ 7].
Recently, through an unsupervised transcriptome analysis, we discovered a molecular classification of ccRCC with four robust subgroups (ccrcc1 to 4) related to previous molecular classifications [ 2, 3] and associated with outcome on sunitinib [ 4].
We then compared these lists to a matrix of 90 user-defined gene sets (Table 3) belonging to various molecular classifications (see methods for details).
According to the molecular classification of breast tumors, we have determined two different subtypes of cell lines, luminal and basal-like, and isolated a subset of genes that discriminates both subtypes.
We assessed a molecular classification as correct if it matched the prototypic subtypes.
In the first section we discuss the molecular classification of sporadic tauopathies, with a focus on describing clinicopathologic relationships.
