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To identify significant differentially expressed transcript tags that distinguished the two groups, we also selected for a fold difference ≥5, a minimal tag count in the corresponding group ≥5 counts, and a P-value≤0.05 resulting in 243 differentially expressed transcripts.
In contrast, the SAGEmap algorithm [ 20] computes a posterior distribution for a fold ratio.
Figure 3 shows the results of the three compared methods for a fold change threshold of 1, results for fold change thresholds 1.5 and 2 are shown in Figures S1 and S2 in Additional File 1.
A microarray analysis of geneticin-treated versus -untreated cells revealed a broad transcriptional response totaling 705 genes (selected for a fold change >1.2, Benjamini Hochberg corrected P-value <0.05; Supplementary Figure S2a).
Probe sets with p < 0.05 after False Discovery Rate correction by the method of Benjamini and Hochberg [ 35] were further filtered for a fold change greater than 1.25 in at least one pairwise comparison.
The number of genes highly modulated in control berries (567) was small in comparison with previous studies [ 22, 40] but this reflects our stringent application of the requirement for a fold change > 5.
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Peter Berkowitz's story went viral after he explained in an op-ed for the Guardian that his solution to the city's housing crisis was to pay $400 a month to live in a tiny pod that he built in his friend's place – a semi-private wooden home with enough room for a fold-down desk, a mini bed and a reading light.
The remaining sequences were assigned as either other endogenous small RNAs or miRNA candidates and used for a fold-back structure prediction.
Thirty percent of the genes whose transcription was significantly decreased 30 min after DTT addition (p-value < 0.01 for a fold-change > 1.5) were predicted to encode secretory proteins (Additional file 1: Table A1.3).
For samples with a fold-change of 1.5-2, we used a cutoff of 50 counts, for fold-change of >2 we used a cutoff of >15 counts and >8 counts for a fold-change >4.
For a fold-change cut off of 1.5 (corrected p < 0.05), 479 out of 623 Z-linked genes on the array (75.2%) showed male-biased expression in at least one tissue.
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