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For hierarchical analysis, genes with greater than two fold changes in expression with 250 nM ganetespib were clustered using established algorithms in Cluster [50].
Given that previous studies have used a robust system to select alternative splicing events and only weak expression of eyeless was detected in SL2 cells (present study), it is likely that the two fold changes in the ey/ey(2a) ratio was below the threshold to be detected by Blanchette et al. [54].
Differentially expressed miRNAs were those that had at least two fold changes between the cultivars and their wild progenitor.
Two fold changes are compared: A) between the segments 3 1 and B) between the segments 3 2.
Genes with P ≤ 0.05 and at least two fold changes in the level of expression were regarded as significantly differentially expressed.
In comparing the SD and LD conditions at the two developmental stages, 183 DEGs with two fold changes were detected P < 0.05.
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The show's goals were two fold: change the world and show off my collection.
With a cut off two fold change and FDR significance score < 0.05, differentially expressed genes (DEG) were identified from the three comparison groups (Additional file 18: Figure S11a).
A subset of 130 genes with greater than two fold change in three or more data points in the E1 and E2 experiments were selected.
GOstat [23] was used to search for significant GO terms for the significant genes with at least two fold change in expression.
A total of 60 contigs showed greater than two fold change in expression level (p<0.01) in vernalized versus non-vernalized leaves.
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