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Analysis of pathway regulation by subtype indicated Wnt/β-catenin as the most commonly upregulated pathway in TNBC subtypes (Additional file 3: Figure S5).
IL-1ß and IL-6 were the most commonly upregulated ALI-related genes that were cited as lung injury related in 287 and 173 references, respectively (Table 2).
Cyclin D1, regulated by the NF-κB pathway, is overexpressed in more than 50% of breast cancers, and is identified as one of the most commonly upregulated proteins in breast cancer [ 39, 40].
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However, CLS extension for the mba1∆ and bna2∆ mutants was not nearly as extensive compared to CR, ade4∆, INAM, or the CR-concentrate, making it possible that most of these commonly upregulated genes only hold predictive value in cases of more extreme CLS extension.
A comparative analysis of the wheat- and rice-responsive transcripts for orthologous genes under Pi-starvation revealed commonly upregulated transcripts, most of which appeared to be involved in a general response to Pi starvation, namely, an IPS1-mediated signalling cascade and its downstream functions such as Pi remobilisation, Pi uptake, and changes in Pi metabolism.
To explore the biological significance of the transcriptome response shared by the two cell lines, z-score reports containing the most significant GO terms were generated from the commonly upregulated (Table 1) and downregulated (Table 2) genes.
This file contains Supplementary Table 1: Commonly upregulated genes in Fermt2, Actg1 and Actb K.O.
c, KEGG pathway enrichment analysis for genes commonly upregulated in Fermt2, Actg1 and Actb knockout compared to wild-type cells.
The mTOR pathway and the enzyme telomerase are two key players commonly upregulated in cancers.
A comparison of the molecular, cellular and functional characteristics of three congruent patient-specific cell types for the modelling of Charcot−Marie−Tooth 1A reveals commonly upregulated chemokines.
EPOP is commonly upregulated in human cancer, and its loss impairs the proliferation of several human cancer cell lines.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com