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There was no significant difference observed between the normal samples and the DCIS and stage I tumors.
Moreover, no statistical difference was found between the normal samples and the histological groups HUT, ADH, FA and ALH regarding SMA and CD34 staining pattern.
As shown (Table 3) there was no statistical difference between the normal samples and the histological groups HUT, ADH, FA, ALH, LCIS and low grade DCIS (DCIS-L) regarding SMA and CD34 staining.
The cytoplasmic scores for Bag-1 intensity were not significantly different between the normal tissue samples and the SCC samples (P=0.272; Figure 2H), whereas there was a highly significant difference in nuclear Bag-1 staining between the normal samples and SCC samples (P<0.001; Figure 2G).
To further analyze our results we compared the expression levels of the 14 down-regulated microRNAs between the normal samples (n = 59), the classical variants (n = 323) and the follicular variants of PTC (n = 99) in the TCGA dataset (Fig. 6a).
Less than 1% of the bands differed in intensity between the normal samples from different patients, indicating that the differences observed between the normal and tumour samples were due specifically to the development of the tumours and not due to either patient polymorphism or PCR-derived artefacts.
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Random-variance paired t-tests were used to determine which genes are differentially expressed between tumour samples and the normal samples.
Statistical testing between the indicated samples and the normal samples are shown in Figure 8B.
The relative fold-change between the aggregate expression in the normal samples versus tumors (primary and metastases) is also presented.
The mean difference between the matching normal and tumour samples (45 out of 53) was 21.6%, with a consistently higher methylation percentage in the normal samples.
For the HYS group, we were only able to calculate a ratio between the averaged normal samples and one sample with AZFc due to the fact that possible replicates had been sorted out by the sample selection procedure.
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