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After a year out of football, Price took over a Miners' program coming off three consecutive two-win seasons.
To understand the function of the SOX2 binding genes, we performed a GO analysis using the GO miner program using evidence level 3 of molecular functions.
In order to identify probe sets with significant intensity differences, the method applied to the unaffected control data set vs. the LGMD2A data set was Benjamini-Hochberg method using Stat Miner program (Integromics).
Outputs of size-calling files were automatically edited with the FP Miner program as described elsewhere [ 44].
Because the CGH-Miner program utilizes a moving-average method for calculating significance, copy number changes of single isolated genes are not detected.
Eight separate S288C self-self hybridizations were used as "NN" controls in the CGH-Miner program, giving a robust baseline to determine the shared copy number changes in the wine strains.
The CGH-Miner program [ 68] was installed and employed as described in the CGH-Miner User guide and Manual [ 100].
Values shown in bold text were determined by the CGH-Miner program to be significantly depleted or amplified as indicated.
When the CGH-Miner program [ 68] generated the consensus plot shown in Fig. 2, it simultaneously created a file showing the genes that are significantly altered in copy number relative to "normal" (self-self) arrays; an abbreviated list of these genes with significantly-altered copy number are given in Table 2.
The final list of genes in the "commercial wine strain signature" is given in Table 2; it is comprised of a subset of those genes for which a statistically significant change in copy number, either depletion or amplification, occurred in at least 3 of 4 strains, as determined by the CGH-Miner program.
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