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The biologically relevant interactions between morphogens and heparan sulfate are optimized by nature for both binding and release, and depend on the precise micropatterned structures of 2- and 6-O-sulfate moieties of heparan sulfate chains (Ashikari-Hada et al. 2004).
To be able to employ the most suitable co-expression distance measure for our analysis, we evaluated the ability of four popular gene co-expression distance measures to detect biologically relevant interactions between pairs of genes.
Beyond validating our computational predictions, our in vitro experiments also suggest the usefulness of iDTP for various applications: The case of the CoA-hPPARγ illustrates how iDTP might be used to reveal biologically relevant interactions between small molecules (ligands, cofactors or metabolites) and cellular proteins.
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While EF-1α is one of the most abundant proteins in the cell and is known to artificially show up in large-scale screens searching for protein protein interaction, our data as a total gave very strong evidence for a specific and biologically relevant interaction between MID1 and EF-1α.
Only two-way, biologically relevant interactions were considered (between immune parameter and body size or condition).
The links between the cliques showed biologically relevant interactions: an inverse relationship between HDL cholesterol and the triglyceride clique (r < -0.3, P < 10-16), a connection between triglycerides and body mass via C-reactive protein (r > 0.3, P < 10-16) and intermediate-density cholesterol as the connector between lipoprotein metabolism and albuminuria (r > 0.3, P < 10-16).
Many more interaction datasets are required to distinguish between conserved and non-conserved (but biologically relevant) interactions and separate them from false positives and false negatives.
To demonstrate the power of CSILRR for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity.
The team demonstrate the power of this network for detecting biologically relevant interactions by predicting and validating the function of previously uncharacterized LRR-RKs in plant growth and immunity.
To improve biologically relevant interactions both for binding and release by tissue heparanase, there is a shift away from using heparin as a global substitute in favor of more biologically appropriate forms of heparan sulfate (Whitelock and Iozzo 2005).
This exemplary case study can not be seen proof that many of the other high ranking predictions will also be true physical and biologically relevant interactions.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com