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A transcript was considered upregulated if its mean expression ratio was larger than 0.5 and the P-value of the t-test was less than 0.05.
A gene was considered upregulated (respectively downregulated) if it had a M-value > 1.0 (resp. < -1.0) and a p-value smaller than 0.01 in a one sided one-sample t-test.
A miRNA was considered upregulated if its Cq value was < 25 in the NSCLC sample and its concentration showed at least a 2-fold increase in the NSCLC sample compared to the control sample.
For example, if the mean normalized value was higher in the summer group than the migrant group, then the gene was considered upregulated in summer butterflies.
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28 Genes whose log fold change is +2 and above is considered as upregulated and −2 and below as downregulated.
The miRNAs with values of log2 ratio (Na200/CK) > 0.5 and < −0.5, along with the p-value of < 0.05, were considered as upregulated and downregulated during salt stress, respectively.
A gene was considered as upregulated or downregulated if it showed 2-fold change relative to the control considering at least three out of four last probes (that are downstream of the translational start site) in both biological replicates.
The miRNAs with a differential expression (fold change) of >2 are considered as upregulated and are highlighted in red, while miRNAs with fold change <0.5 are considered as downregulated and are highlighted in blue.
A gene was considered as upregulated or downregulated if it showed a minimum of 2.5 fold change relative to the control in at least three out of the four last oligonucleotides in all biological replicates.
Genes were considered as upregulated if (i) the corresponding signal intensity was at least two-fold increased as compared with wild type and if (ii) the FDR Q-value was below 0.10.
The criteria we set for a gene to be considered as upregulated or downregulated were a RA/non-RA ratio higher than 3 or lower than 0.3, respectively, and a 95% confidence interval below 10% (criteria as [ 30]).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com