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When HGF was the stimulus (H. pylori input was set to 0 and HGF input set to 1), CNA finds only 6 knockout targets for ERK1/2 repression (HGF, c-Met, HGF/c-Met, ERK1/2, MEK, Raf1).
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Figure 1 illustrates the concepts of CNA region and CNA unit, where two CNA regions contain 10 and 3 CNA probes, respectively, and the first CNA region is further split into three CNA units due to two breakpoints within the CNA region.
We found 26 CNA regions (26 deletions and no amplification) in primary tumors and 235 CNA regions (173 deletions and 62 amplifications) in metastases.
A total of 145 CNA ≤2 Mb were detected.
Among them, there were 81 CNA mapped to Mendelian CNV.
Twenty-five patients (80%) with 104 CNA exhibited 41 gains and 63 losses (table 4).
Losses at 4q and 18q were found to be associated in one study [9] but this was not replicated in a recent analysis [10], which identified 7 CNA associations and 6 anti-correlations.
The Myc-CnA and Myc-CnB expression constructs under the CMV promoter were subcloned from 'pET15b CnA CnB' (Addgene).
This would suggest that 8q and 16q CNA's are likely to be early events in tumourigenesis.
Therefore, the MYC−/ TP53+ and MYC+ and/or TP53− CNA patterns may be signatures of dormant and aggressive TUBs, respectively [ 16].
30 We analyzed the logical model with the software CellNetAnalyzer 9.0 (CNA), a MATLAB package for graph-theoretical and logical analyses (The MathWorks, Natick, MA, USA).
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