Dear Yiota and Dimitris,

comparing the RNAseq and the PolysomeSeq data, there are
several observations:

a) Histograms showing the correlation of normalized expressions per gene
between transcriptome RNAseq and polysome profiling show an expected higher
polysome expression at low RNAseq transcription for the WT
(Figures: wt0h-PolysomeVSRNAseq-hist.png,
wt2h-PolysomeVSRNAseq-hist.png,
wt6h-PolysomeVSRNAseq-hist.png).

This is visibly lower in the KO at 0h
(Figure: Ko0h-PolysomeVSRNAseq-hist.png),

slightly lower in the KO at 2h and 6h
(Figures: Ko2h-PolysomeVSRNAseq-hist.png , Ko6h-PolysomeVSRNAseq-hist.png)

and indifferent comparing wtIFN and koIFN and
(Figures: wtIFN-PolysomeVSRNAseq-hist.png, KoIFN-PolysomeVSRNAseq-hist.png)
wtIL4 and koIL4
(Figures: wtIL4-PolysomeVSRNAseq-hist.png, KoIL4-PolysomeVSRNAseq-hist.png)

b) The differential expressions in transcriptome RNAseq and polysome profiling
can be combined in log2 foldchange scatter plots.
In the plot 0h-wtVSko-PolysomeVSRNAseq_perGene.png for all expressions measured at 0h,
the x-coordinate shows the difference betweeen the log2 of the normalized reads per gene in WT RNAseq and
the log2 of the normalized reads per gene in WT PolysomeSeq, and
the x-coordinate shows the difference betweeen the log2 of the normalized reads per gene in KO RNAseq and
the log2 of the normalized reads per gene in KO PolysomeSeq.
As the differences in log2 values correspond to foldchanges, the foldchanges due to the type of measurement
can be compared between WT and KO.
Genes right of the vertical x=0 axis correspond to RNAseq expression higher than Polysome expression in the WT.
Genes above the horizontal y=0 axis correspond to RNAseq expression higher than Polysome expression in the KO.
All genes with a difference between the 2 foldchanges >=5 (corresponding to a 32 fold difference) are shown
with their name.
It is obvoius that the number of genes with a higher RNAseq expression than PolysomeSeq expression is much larger
for the KO than for the WT.

The foldchange differences between WT and KO increase form 0h to 2h (Figure: 2h-wtVSko-PolysomeVSRNAseq_perGene.png)
and further from 2h to 6h (Figure: 6h-wtVSko-PolysomeVSRNAseq_perGene.png).

If you can confirm that the genes in the quadrants show some interesting enrichment,
we can further extend this analysis.

BW,
Martin