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For each gene, the relative total expression level from all expressed homoeoloci was calculated from the total number of reads mapping to the gene sequence, normalized by both the sequence length and the total number of mapped reads in the sample, to give a standard RPKM measure of expression (reads per kb per million aligned reads).

We performed a gene enrichment test from Babelomics tools (Fatigo) on our data where significantly up and down-regulated groups of functionally related genes were identified from all expressed genes according to differential expression between the two comparisons (with higher or lower expression in ob/ob vs. WT but without changes in POKO vs. WT mice).

Global transcriptional trends derived from all expressed genes, instead of differentially expressed genes alone, were examined, allowing for a higher discriminating power in the functional portrait.

For genes with multiple probes, the median value from all expressed probes was used.

Based on the views expressed in a survey such as ours, a compromise can be obtained, which is acceptable from all expressed points of view.

Additionally, use of sonication for fragmenting cDNA allowed us to sequence tags from all expressed genes, unlike restriction enzyme based methods, which require the enzyme recognition site in the gene to get a sequence tag.

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The EB-derived cells from LQT2 iPSC and control iPSC lines all expressed markers from the three different embryonic lineages: endoderm, ectoderm and mesoderm (Fig. 2F).

Again, the FLAG constructs appear greatly reduced compared to both the OmpA without insertion and the OmpA with an SA-1 insertion, all expressed from plasmid.

These genes were all expressed from PL-lacO1 (pIAA16, pIalong along with kivd and ADH2 (pIAA13; Table  2).

The other spliceosomal snRNAs are all expressed from single copy genes.

Estimates of the number of circadian-regulated genes in Arabidopsis range from hundreds [19] to essentially all expressed genes [20].

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