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Strikingly, we have found that promoters of the most upregulated putative late response genes had low-occupancy promoters with a RNAPII positioned immediately downstream of the TSS (Additional file 1: Figure S8), and conversely that at high-occupancy promoters p65 binding had less impact on transcription.
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Interestingly, the most upregulated gene encodes a putative pirin protein.
The most upregulated gene in this group was the putative transmembrane phospholipid-transporter ATPase Class II type 9A (and9A) and consistently upregulated were also the tumor necrosis factor receptor-associated factor 1 (that1), that was earlier shown to be upregulated in EBV infected cells [24], [25].
We identified CD44 as the most upregulated marker gene for colon cancer among 57 putative biomarkers.
P. gingivalis actively upregulated putative virulence factors (34 in total) while T. denticola, with three upregulated putative virulence factors, and T. forsythia, with one, seem not especially active at this stage (Additional file 6: Table S4).
Notably, our study identified MMP-1 as the most upregulated marker gene for breast cancer, opening up the possibility, after follow-up validation studies, for its use as a putative predictive marker in screening for breast cancer.
Complex I was the most upregulated complex and not stoichiometrically associated to the other complexes.
Of these, IFN-stimulated gene 15 (isG15) is one of the most upregulated, suggesting its possible involvement in the pathogenesis of this disease.
IL-1β and IL-8 were the most upregulated genes and to a lesser extent TNF-α.
With miRNA-seq analysis, we find that miR-147b is the most upregulated microRNA in osimertinib-tolerant and EGFR-mutated lung cancer cells.
Rarβ2 is the RAR subtype whose expression is most upregulated in response to ligand and its localization in the trunk somites positions it at the right time and place to respond to embryonic retinoid levels during somitogenesis.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com