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Do different fusion methods tend to identify functional links between the same proteins?
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no difference (fold change of less than 1.2 or more than 0.8); ASt/nASt, fold change of all differentially expressed proteins between ASt and nASt; ASt/NC or nASt/NC, fold change of the same proteins between ASt and NC or nASt and NC as those differentially expressed in ASt/nASt.
Although relative quantification methods are useful to compare the same proteins between multiple biological samples, they do not provide the possibility to directly compare the data with other datasets or compare different proteins within a dataset with each other and they, by definition, do not provide absolute quantitative data.
The finding that synthesis of mitochondrial proteins was consistently higher than other proteins within the same tissue and that synthesis rates of the same proteins varied between tissues (e.g. higher rates in soleus versus plantaris) demonstrates that protein synthesis can be differentially regulated within and between tissues [34], [34,38].
Here we observed eight out of ten of the same proteins shared between the two data sets.
The relationship between correlated mutations and spatial proximity (not always direct contact) has not only been found between residues in the same protein but also between residues in different proteins (Pazos et al, 1997; Yeang and Haussler, 2007; Burger and van Nimwegen, 2008).
Error factor and p-value estimates presented in the supporting information provide a means of assessing consistency between peptides within the same protein.
Of these 430 interparalog edges, 258 are interactions between members of the same protein complex (~ 60%).
Therefore, the observed variation of nucleotide polymorphism between regions within the same protein may also reflect such a phenomenon.
To highlight potentially interesting isoforms displaying differential behavior, a correlation score was calculated between isoforms of the same protein.
There is a remarkable large variation between sequences of the same protein in both the CBP and the H&S methods.
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