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To enhance the specificity of the network to the selected disease, it has been manually removed after filtering.
Thirdly, it is beyond the scope of this paper to explore the cultural specificity of the network typology between or within groups of South Asians (Gujaratis, Punjabis and Sylhetis).
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In contrast to the specificity of the networks for the darkgrey and lightgreen modules, the EnrichmentMap for the probe-based analysis gene set shown in Additional file 2: Figure S4 is less tightly connected with many nodes having zero connections.
Interestingly, it was noted that while increasing PCC threshold had no apparent effect on specificity of individual microarray networks, specificity of the Conserved network increased up to two-fold with PCC values, suggesting that gene pairs with high PCCs in the Conserved network are likely to be well-annotated molecular entities.
The sensitivity and specificity of the iNJ661v network model were substantially larger than those of the other two networks regardless of the threshold used to determine essentiality.
Further attempts to integrate diverse genomic dataset will seek to improve the sensitivity and specificity of these network predictions.
To study the specificity of the calculated network, we plotted the total number of correct interactions detected as a function of T in Fig. 1b.
The spectral specificity of the observed network modulations was investigated by calculating the frequency-resolved degree over all significant connections within each frequency band.
Phenotype specificity of the Conserved network was estimated by comparing it to gene co-expressions inferred from the Normal mouse transcriptome (3983 genes, 91544 interactions; PCC≥0.70) [ 18].
We chose to explore 1st (direct) and 2nd (through another protein) degree PPIs among the protein products of the focal genes to gain complexity without losing specificity of the overall network.
We validated the subtype specificity of the driver-networks and tested the value of the integrated analysis by knocking down 30 driver-network genes and comparing the results with knockdowns of 10 differentially expressed, non driver-network genes in a panel of breast cancer cell lines.
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