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When a twofold cut-off value was applied as criterion to distinguish differentially expressed transcripts between grain and sweet sorghum, a total of 195 transcripts were identified, with 132 transcripts being down-regulated and 63 transcripts up-regulated in Rio, respectively (Electronic Supplementary Material Tables S1 and S2).
By applying a twofold cut-off value as a parameter to filter out differentially expressed transcripts, a total of 195 probe sets were identified, of which 63 corresponded to transcripts that were up-regulated (51 genes) and 132 (103 genes) corresponded to transcripts that were down-regulated in the sweet sorghum Rio line, respectively.
The TCF/LEF signature consisted of 74 genes that were responsive to dominant-negative TCF-4 (twofold cut-off) in colon cancer cells.
Previous studies have shown that using arbitrary twofold cut-offs to determine presence or absence of genes is more conservative than other methods such as GACK or standard deviation from the median [ 48].
(11) The examination of overlapped genes between the criterion and the predicted targets led to identification of 16 candidates as potential targets of miR-493 (Fig. 1a), whereas only eight genes were identified if the previous criterion with a twofold cut-off was applied.
(11) In order to look for crucial target genes of miR-493, we used a searching criterion that differs from the one used in our previous studies: statistical significance (P < 0.05), instead of twofold cut-off, was used to select candidate genes through expression analyses of miR-493-transfected Hcancercells cancer cells (Fig. 1a).
The major approach is twofold: edge-cut method and vertex-cut method.
A twofold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value<0.01), robust and reproducible.
If the twofold increased risk cut-offs were used, 8.8% would be diagnosed by OGTT for a total of 10.5% including the markedly hyperglycaemic group.
Taking a twofold difference as the cut-off point, microarray analysis detected 19 upregulated and 9 downregulated miRNAs in the three pairs of CCA and corresponding non-tumor tissues.
To select transcripts for further analysis, an additional expression cut-off of twofold was applied.
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