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Additional signatures distinguished upregulated and downregulated genes.
Differential binding and epigenetic patterns distinguished upregulated and downregulated genes.
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Pathway cluster P9 is distinguished as commonly upregulated in tumor samples.
We identify a subset of genes preferentially expressed in nectaries, and distinguish the gene complement upregulated in actively secreting nectaries compared to immature and non-secretory nectaries.
Within the 3120 genes, five patterns (further called "transcript groups") could be distinguished: 1213 genes were significantly upregulated both on wheat straw and on lactose (Table 1); 1619 genes were upregulated only on wheat straw (transcript group A), in contrast to only 288 genes that were upregulated on lactose (transcript group B) only.
These genes are described hereafter as not downregulated (NDR) and not upregulated (NUR) respectively, to distinguish them from genes, which are genuinely modulated by defoliation.
The Alk4 receptor (Acvr1) was also found in the list; however, it cannot be distinguished from the exogenous Alk4*, which is upregulated by Dox/rtTA, and therefore, cannot be included in our list of Smad2/3 targets.
Of the genes distinguishing Ta tumours from normal bladder biopsies, most were found upregulated.
For instance Wachi and coworkers identified a high network centrality for genes that are upregulated during lung cancer as a distinguishing topological feature to enable placement of cancer genes into the global and systematic context of the cell (Wachi et al., 2005).
Near infrared fluorescent (NIRF) probes activated by biomarkers upregulated in adenomas (eg, cathepsin B) are potentially powerful tools to distinguish premalignant or malignant lesions from benign or inflammatory lesions.
The urea-cycle enzymes distinguish themselves from most other genes in the liver in that they were upregulated in expression throughout the period of fasting that was studied.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com