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. 2011 Aug 26;6(8):e23016. doi: 10.1371/journal.pone.0023016

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Milenković et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Left: Direct neighborhood of ZAP90, a cancer and HIV gene, in the human PPI network [28]. Its degree is 48 and it is ranked as the top gene with respect to DC. Right: Direct neighborhood of PRKACA, an HIV gene, in the network. Its degree is 145 and it is ranked as the top gene with respect to DC. Both proteins have the same GDC and are ranked as top genes with respect to GDC. Hence, GDC rewards the ranking of a low-degree gene if its 4-deep neighborhood is dense (ZAP90) and penalizes the ranking of a high-degree gene if its 4-deep neighborhood is sparse (PRKACA). (For the esthetics of the figure, we only show 1-deep neighborhoods.)

Inline graphic — Left: Direct neighborhood of ZAP90, a cancer and HIV gene, in the human PPI network [28]. Its degree is 48 and it is ranked as the top gene with respect to DC. Right: Direct neighborhood of PRKACA, an HIV gene, in the network. Its degree is 145 and it is ranked as the top gene with respect to DC. Both proteins have the same GDC and are ranked as top genes with respect to GDC. Hence, GDC rewards the ranking of a low-degree gene if its 4-deep neighborhood is dense (ZAP90) and penalizes the ranking of a high-degree gene if its 4-deep neighborhood is sparse (PRKACA). (For the esthetics of the figure, we only show 1-deep neighborhoods.)