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We also removed genes not expressed in any tissue beyond expression threshold, resulting in 15,447 genes that entered the analysis.
An RPKM (Reads per Kilobase per Million reads) cutoff value of 0.1 was set to declare a locus expressed, resulting in 21,530 loci above the expression threshold.
When a 2-fold difference in expression threshold was applied, 73 genes were significantly differentially expressed in common between the two techniques.
By applying a 5-fold lower expression threshold in a specific tissue, we identified miRNAs that specifically lower expressed (or avoidant) in a given tissue.
In particular, despite the expression threshold employed for defining the expression of a transcript, several thousands of novel transcripts were still identified (Figure S1a c and Table S1).
We calculated the proportion of known and novel transcripts for each RNA-seq sample with an expression threshold of TPM > 1.0 and averaged the values for corresponding replicates from each developmental stage.
Though the expression of RCT1 transcripts was observed to be stable and constitutive, and unaffected by pathogen infection, a certain expression threshold for RCT1 AT seemed to be essential for effective resistance19.
Indeed, in the strain without mutation, the expression threshold necessary to excision is very low.
Microarrays were normalized using the MAS5 algorithm, and expression threshold and ceiling values were applied as described [8].
The results were first filtered for probesets that were detected above an expression threshold ("MPC-5 transcriptome").
To further eliminate genes near background in these normalized data we set a median expression threshold value of 90 for either CR or HIGHCAL.
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