To focus on the genes significantly changed under drought compared with the well-watered condition, we only selected those whose expressions have: 1) more than two fold changes; 2) with q-values less than 0.01.
Thus, having a set of endogenous reference genes that are stably expressed at different levels makes it possible to help select those whose expression is comparable to the target genes.
In order to create a gene set that best predicts the pharmacological response to IFNß we selected those genes whose expression shows the most significant negative correlation between baseline and biological response (with a cut off of p<0.01 and R<−0.65).
When microinjecting exogenous molecules, such as PAMPs or drugs, check different Renilla reporter plasmids and select those with consistent expression.
For live imaging, hosts were screened at 40 hpf on an upright fluorescent microscope to select those where Atoh7 expression has just started.
While this cutoff is arbitrary, it specifically selects those genes whose expression values best distinguish children with disease from healthy children.
We selected those microRNAs whose expression was up- or downregulated with a fold change greater than four in at least one of the four precursor populations when compared with the CD34 HPCs.
To identify genes regulated by phytochrome in tomato seeds we selected those genes whose expression was statistically affected by pulses of R compared to FR light if: 1) the p-value was ≤ 0.05 in the one sample t-test and 2) there was at least a 1.5 fold change in expression.
For each metric, we selected those DEGs whose expression profiles met three criteria: (i) the FPKM value was ≥1 in either of the libraries, (ii) log2 (FPKMsalt/FPKMcontrol) was > 1 or < -1, and (iii) the adjusted p-value (FDR) was < 0.05.
Microarray data can be used to identify potential RGs by modeling the expression data to select those with the most stable expression [ 9- 11].
As for the analyzed gel spots, we selected those fulfilling two criteria: expression change of at least 1.3-fold compared to the control group and a significant t test result (n = 6 in each group, p<0.05).
