Sentence examples for molecular subtypes we from inspiring English sources
To map the 176 Rembrandt samples with survival data to the relevant TCGA molecular subtypes, we extracted the gene symbols from the 840 gene centroid developed previously [6].
Analysis of patient data for the 4 molecular subtypes we identified in the Thompson dataset confirmed our results for differences in metastasis, histology and age at diagnosis (Figure 7).
For other molecular subtypes, we did not find significant differences in survival between groups receiving treatment with CAF or CMF (Additional file 1, Table S5).
When we compared different intrinsic molecular subtypes we found 46 miRNAs that were specifically expressed in one or more intrinsic subtypes.
For the molecular subtypes, we conducted a case-only analysis comparing Luminal B, HER2+, and triple-negative cases with Luminal A cases.
In order to compare the overlap between the groups of molecular subtypes, we first had to divide the tumors into robust and reproducible groups delimited by REST function.
For accurate molecular subtyping, we present an alternative approach to gene centering that incorporates a routine data transformation step prior to subtyping.
To better characterize the claudin-low molecular subtype, we identified those genes differentially expressed in claudin-low tumors compared with other tumors or subtypes.
Finally, in the area of gene expression for classification of molecular subtype, we considered correlation used for validation in [ 27] (CVal), and with centroids for normal (CNorm), ErbB2+ (CERBB), Lumina A (CLumA), Lumina B (CLumB), and basal (CBas) from [ 6].
To evaluate whether site of distant metastasis is determined by specific methylation patterns of the primary tumor or rather by inherent molecular subtype, we performed logistic regression comparing the different metastatic sites one by one with quantitative methylation status of individual genes and molecular subtype as variables in the model.
We have no prior knowledge of whether the factors adjusted for influence molecular subtypes, so we chose a conservative approach.
