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The small-world coefficient was calculated as [(C÷ C R ) ÷ (L÷ L R )], where C R and L R are the mean clustering co-efficient and average shortest path length, respectively, of equivalently-sized randomly-generated networks [ 26].
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To this aim, we calculated the network average clustering co-efficient (NACC) between the mitotic checkpoint and progression modules in luminal samples with known TP53 status [ 48].
Comparing the core response network to 1000 randomly generated networks of an equivalent size (see Methods) revealed that the clustering co-efficient (C) of the former (0.102) was ~7.3 times the mean C value (0.014) of random networks, while the average shortest path lengths (L) were similar (3.913 and 4.738, respectively).
Like many other real world complex networks, the Natural Language networks also obeys the small world property and showed high clustering co-efficient.
Changes in the various topological properties including clustering co-efficient, closeness, betweenness, page rank, etc., between different K sizes can be found in Additional file 1: Figure S1.
The comparative study of antimicrobial activities of the samples has been considered for three different parameters like Mean deviation (MD), Co-efficient of Mean Deviation (CMD) and Karl Pearson's Co-efficient of Correlation (r).
Ranking of the probes according to the mean correlation co-efficient was then used to determine which genes were specifically co-expressed with the identified PSII-related cluster and to the remaining lumen protein genes.
In order to identify genes showing high co-expression with selected lumen protein genes the mean correlation co-efficient for the selected lumen protein genes and any given probe was calculated.
The lowest DICE co-efficient between VBM and ROI ventricle measurements was 0.92, and the mean DICE co-efficient between VBM and ROI ventricle measurements was 0.927 for left lateral ventricle and 0.948 for right lateral ventricle indicating substantial overlap between the 2 techniques as shown in Figure 1.
The mean correlation co-efficient was 0.88.
The mean correlation co-efficient was determined and represents the mean correlation in signal ratios observed between data from any two microarray slides.
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