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It should be noted that the genes that the HubDetector identifies are the genes changing expression most often between different cellular states these, differ from the genes with the highest variance as studied in Bilu and Barkai (2005).
Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states.
Networks of phosphorylation-induced signaling can result in complex effects such as signal amplification, feedback inhibition or induction of cyclical oscillation between different cellular states [5] [8].
The "L" isoforms encompass a functional immunoreceptor tyrosine-based inhibitory motif (ITIM) and both CEACAM1-L and CEACAM1-S isoforms are often co-expressed in the same cell, with expression ratios varying between different cell types and between different cellular states [ 18, 41].
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A TSR score can be seen as the degree of activity of the regulator in different cellular states or phenotypes.
This suggests that miRNA-lincRNA target can be specific to different cellular states.
Mitochondria are highly dynamic organelles and attain different shapes reflecting different cellular states, during the lifetime of a cell.
Thereby a single genome can be reliably utilized in many different ways because epigenetic modifications fix the different gene expression patterns that define different cellular states [ 2- 4, 13].
Quantitation of differential membrane protein abundance across different cell-envelope compartments, or even under different cellular states, can be achieved using fluorescent protein-reactive dyes before 2D-PAGE.
One tool that goes further in the direction of simultaneously comparing different cellular states or different tissues is Arena3D [ 106, 107].
Therefore, attempts to identify cell subpopulations based on multiparametric proximities may actually identify different cellular states but not different types of cells.
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