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(G ) Average relative levels of the most downregulated proteins, log2 ratios ≤ −0.4, in disomes- UBP6 (blue) and disomes- ubp6Δ (red) compared to wild-type cells.
(C ) Average gene expression levels of the most downregulated proteins, log2 ratios ≤ 0.4, in disomes (blue) and disomes- ubp6Δ (red) compared to wild-type cells.
CCL3, IL1β, CXCL1, CSF2, CSF3, IGFBP1, IL1α, IL6, IL8, CCL20, PLAUR, PlGF and VEGF were strongly upregulated in IIB-BR-G-MTS6 while CCL4, ICAM3, CXCL12, TNFRSF18, FIGF were the most downregulated proteins in the metastatic cell line.
-wrap> Interestingly, CBR2, also known as 'mouse lung carbonyl reductase' (MLCR) was one of the most downregulated proteins over the culture period, with very similar kinetics compared to proSFTPC expression.
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Many cellular functions were affected by furfural, with the most highly downregulated proteins involved in cell wall biosynthesis or sporulation.
This impairment may be linked to elevated FOXM1 expression as FOXM1 is known to abrogate GATA3 activity [ 47] and GATA3 was the most frequently downregulated protein of this set of proteins in GU.
Also, most of the downregulated proteins were non-oscillating.
Table 1 shows the most up and downregulated protein coding genes (excluding pseudogenes) in the translatome fraction and Additional file 4 shows all the differentially regulated genes at the transcriptome and translatome levels.
The most downregulated genes including Fatty acid binding protein 4, adipocyte (FABP4), adiponectin (ADIPOQ), and retinol binding protein 4 (RBP4) were known to be involved in lipid metabolism.
The downregulated enrichment or DRE ranks from most downregulated to the least downregulated.
Moreover, GO analysis showed that protein biosynthesis was the most downregulated biological process term.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com