Constructing Weighted Gene Correlation Network on GPUs

Here we constructed a weighted gene correlation network in human glioblastoma cells by developing the graphics processing units (GPUs) algorithm. The strength distributions of entire network, housekeeping genes and hubs in protein interaction network were calculated and the differences between them were found. Six definitions of clustering coefficient previously proposed for weighted networks were calculated in this paper and behaved quite differently. Interestingly, the clustering coefficient distributions of housekeeping genes and hubs are similar to that of entire network, as the strengths of them are generally bigger. This work explored how to calculate the network indices in weighted biological networks on GPUs and whether these indices can reflect the characteristics of biological networks.