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None of the features which presented a mutual correlation were excluded from further analysis.
The problem with revealing genes connected with the progressive disease during expression analyses was also noted in other studies, where such correlation were excluded or postulated only for an extremely limited number of genes.
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Examination of the ranking of the different subjects in relation to each of the DDR-related parameters analysed shows a high degree of correlation for all pair-wise comparisons, in both BMPC and PBMC, with the Spearman correlation coefficients ranging 0.83 0.97 if d-globin transcription (which shows a significant but lower correlation) is excluded (Supplementary Tables 3 and 4).
HM allows us to obtain the best QSAR based on F and t test values, which were set in such way that descriptors having more than 0.99 and less than 0.8 correlations were excluded as they may generate an over-optimistic regression.
In a first step, coping strategies with low item-total correlations were excluded.
We performed an initial check for correlations between the 27 variables with Spearman (two-tailed) bivariate correlations and SPSS 10.0, and the parameters involved in the largest number of correlations were excluded sequentially until no correlation remained.
Scores from 3 reviewers with correlation scores more than 2 standard deviations from the average correlation score were excluded from the reference collection (Supplementary Figure S2).
For better comparability between correlations, data were excluded listwise, resulting in n = 91 complete datasets entered into all analyses reported in Table 2.
Group samples with gene expression correlation coefficients ≤0.95 were excluded (one KO sample).
As many of the 470 features turned out to be highly correlated, 128 features with Spearman correlations > 0.98 were excluded from further analyses, leaving 342 features used.
Items with residual correlations exceeding |.25| were excluded regardless of content.
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