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The guanidinium chloride insoluble Alcian blue stained Muc2 band showed no alterations (data not shown).
Analysis of the M10 cells-derived metastatic MT10 and MG10 cells revealed the presence of identical gene alterations (data not shown).
The remaining 10 patients displayed H19DMR-GOM but did not show other causative alterations (data not shown).
Minimal cystic dilation was noted in rare glands, in the absence of any gland crowding or other cytologic alterations (data not shown).
For identification of DNA copy number alterations, data were smoothed using a local polynomial adaptive weights smoothing procedure for regression problems with additive errors (Hupe et al, 2004; Natrajan et al, 2006).
Adult ces-1 plants did not show any obvious BR-deficient phenotypes and measurements of BR levels in these plants did not reveal any statistically significant alterations (data not shown).
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For patients in each subgroup, we identified significantly altered genes against the remaining samples based on the network-smoothed alteration data by SAM (SAM significance analysis of microarrays was originally designed for identifying differentially expressed genes) [ 47].
One of the most successful approaches to discerning the signal in mutation data or in copy number alteration data is to seek out those genes or regions which are altered at a frequency above a background random model.
Sequence mutation and DNA copy number alteration data for all TCGA GBM cases was obtained from the TCGA data portal [48].
(1) More alteration data: the next phase of the TCGA GBM project will be sequencing over 6,000 gene and microRNA targets in several hundred additional GBM cases, as well as a number of tumor and paired normal complete genome sequences.
Approximately 90% of all ras mutations affect the K-ras gene, of which 85% occur in codon 12. K-ras mutations occur in particularly high frequency in adenocarcinoma (20 30%) but sequencing of k-ras and c-raf of our transgenic tumor model did not evidence any sequence alteration (data not shown).
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