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Neighbor overlap is enriched in the yeast interaction network: analysis and implications.

Feiglin A, Moult J, Lee B, Ofran Y, Unger R - PLoS ONE (2012)

Bottom Line: We show that Neighbor Overlap is enriched in the yeast protein-protein interaction network compared with control networks carefully designed to match the characteristics of the yeast network in terms of degree distribution and clustering coefficient.Finally, we demonstrate that pairs of proteins with redundant functions tend to have high Neighbor Overlap.We suggest that a combination of three mechanisms is the basis for this feature: The abundance of protein complexes, selection for backup of function, and the need to allow functional variation.

View Article: PubMed Central - PubMed

Affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.

ABSTRACT
The yeast protein-protein interaction network has been shown to have distinct topological features such as a scale free degree distribution and a high level of clustering. Here we analyze an additional feature which is called Neighbor Overlap. This feature reflects the number of shared neighbors between a pair of proteins. We show that Neighbor Overlap is enriched in the yeast protein-protein interaction network compared with control networks carefully designed to match the characteristics of the yeast network in terms of degree distribution and clustering coefficient. Our analysis also reveals that pairs of proteins with high Neighbor Overlap have higher sequence similarity, more similar GO annotations and stronger genetic interactions than pairs with low ones. Finally, we demonstrate that pairs of proteins with redundant functions tend to have high Neighbor Overlap. We suggest that a combination of three mechanisms is the basis for this feature: The abundance of protein complexes, selection for backup of function, and the need to allow functional variation.

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Schematic view of Neighbor Overlap.In the depicted example nodes A (degree = 7) and B (degree = 5) have 3 common neighbors. According to the definitions in the text, NOcount  = 3, NOnorm = 3/5 and NOjaccard  = 1/3.
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pone-0039662-g001: Schematic view of Neighbor Overlap.In the depicted example nodes A (degree = 7) and B (degree = 5) have 3 common neighbors. According to the definitions in the text, NOcount  = 3, NOnorm = 3/5 and NOjaccard  = 1/3.

Mentions: For example, in Figure 1 NOnorm = 3/5, NOjaccard = 3/9 = 1/3 and NOcount = 3. We note that this definition applies whether proteins A and B have a direct link or not.


Neighbor overlap is enriched in the yeast interaction network: analysis and implications.

Feiglin A, Moult J, Lee B, Ofran Y, Unger R - PLoS ONE (2012)

Schematic view of Neighbor Overlap.In the depicted example nodes A (degree = 7) and B (degree = 5) have 3 common neighbors. According to the definitions in the text, NOcount  = 3, NOnorm = 3/5 and NOjaccard  = 1/3.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3383679&req=5

pone-0039662-g001: Schematic view of Neighbor Overlap.In the depicted example nodes A (degree = 7) and B (degree = 5) have 3 common neighbors. According to the definitions in the text, NOcount  = 3, NOnorm = 3/5 and NOjaccard  = 1/3.
Mentions: For example, in Figure 1 NOnorm = 3/5, NOjaccard = 3/9 = 1/3 and NOcount = 3. We note that this definition applies whether proteins A and B have a direct link or not.

Bottom Line: We show that Neighbor Overlap is enriched in the yeast protein-protein interaction network compared with control networks carefully designed to match the characteristics of the yeast network in terms of degree distribution and clustering coefficient.Finally, we demonstrate that pairs of proteins with redundant functions tend to have high Neighbor Overlap.We suggest that a combination of three mechanisms is the basis for this feature: The abundance of protein complexes, selection for backup of function, and the need to allow functional variation.

View Article: PubMed Central - PubMed

Affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.

ABSTRACT
The yeast protein-protein interaction network has been shown to have distinct topological features such as a scale free degree distribution and a high level of clustering. Here we analyze an additional feature which is called Neighbor Overlap. This feature reflects the number of shared neighbors between a pair of proteins. We show that Neighbor Overlap is enriched in the yeast protein-protein interaction network compared with control networks carefully designed to match the characteristics of the yeast network in terms of degree distribution and clustering coefficient. Our analysis also reveals that pairs of proteins with high Neighbor Overlap have higher sequence similarity, more similar GO annotations and stronger genetic interactions than pairs with low ones. Finally, we demonstrate that pairs of proteins with redundant functions tend to have high Neighbor Overlap. We suggest that a combination of three mechanisms is the basis for this feature: The abundance of protein complexes, selection for backup of function, and the need to allow functional variation.

Show MeSH