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The final layout and analysis of the data was performed using a Pearson correlation cut off of r = 0.9 and the resultant graph clustered using an MCL inflation value of 2.2.
Using a strict correlation cut off (r > 0.85) leaves only three members of the rif1∆ est1∆ class; however, we can see in Figure 4F that the 20 most highly correlated genes display a distinctive MDP.
In order to define the spot's differential expression a linear regression was performed by the software and a correlation cut off was applied and gels with R lower than 0.8 were discarded.
All Pearson correlations with r ≥0.7 were saved to a '.pearson' file and a correlation cut off of r = 0.8 was used to construct a graph containing 20,355 nodes (probesets) and 1,251,575 edges (correlations between nodes above the threshold).
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Neither the pSF-12 PCS, the pUI nor the FES reached the intraclass correlation coefficient cut off of 0.7 that is generally considered acceptable agreement [ 24].
Genefilter package73 was used for correlation (cut-off |0.5|) of miRNAs, and each miRNA was assessed as either a tumor suppressor miRNA or an oncomiR based on its regulatory effects on known oncogenes or tumor suppressors in the RPPA data (Supplementary Table 1).
The dynamic changing topology of the Always Correlated network can be visualised by changing the correlation cut-off incrementally.
Using a Pearson correlation cut-off >0.6 combined with a gene expression log2 standard deviation cut-off >0.9, we identified 34 genes to be positively co-expressed with CCNB1 (Table S1).
All identified tryptic and non-tryptic peptides, greater than six amino acids in length, were first filtered by charge state-dependent cross correlation cut-off (Xcorr) scores as described previously [39], and further filtered using a relatively high confidence PeptideProphet [41] cut-off score of 0.8.
Partially tryptic peptides were additionally filtered by charge state-dependent cross correlation cut-off (Xcorr) scores as follows: a minimum cross-correlation cut-off (Xcorr) of either 3.1, 3.8, or 4.5 for 1+, 2+, or 3+ charge states, respectively.
Researchers employ various item-component correlation cut-off levels above which an item is incorporated into a summated scale.
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