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Table 2 Understanding the factors that affect gene significance.

From: Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome

Data Set No. Samples a.) cor(severity, MEblue)1 b.) cor(severity, SNP)2
Samples with severity scores 87 r = 0.27 (p = 0.011) r = 0.28 (p = 0.010)
Males & HomFemales 76 r = 0.50 (p = 8 × 10-6) r = 0.33 (p = 0.003)
Males with severity scores 23 r = 0.34 (p = 0.113) r = 0.45 (p = 0.030)
Females with severity scores 64 r = 0.26 (p = 0.041) r = 0.17 (p = 0.170)
Homogenized Females 53 r = 0.54 (p = 2 × 10-5) r = 0.25 (p = 0.076)
Second data set (DS)3 33 r = 0.09 (p = 0.638) r = 0.03 (p = 0.846)
Second DS Homogenized3 30 r = 0.38 (p = 0.040) r = 0.15 (p = 0.415)
Data Set No. Samples c.) cor(severity, FOXN1 ) d.) cor(SNP, FOXN1 )
Samples with severity scores 87 r = 0.21 (p = 0.055) r = 0.18 (p = 0.088)
Males & HomFemales 76 r = 0.38 (p = 6 × 10-4) r = 0.23 (p = 0.045)
Males with severity scores 23 r = 0.27 (p = 0.216) r = 0.20 (p = 0.365)
Females with severity scores 64 r = 0.21 (p = 0.101) r = 0.19 (p = 0.137)
Homogenized Females 53 r = 0.44 (p = 0.001) r = 0.24 (p = 0.082)
Second DS3 33 r = 0.28 (p = 0.116) r = 0.18 (p = 0.318)
Second DS Homogenized3 30 r = 0.40 (p = 0.030) r = 0.12 (p = 0.515)
  1. The severity, MEblue, TPH2 SNP, and FOXN1 correlations (r) and p-values (p) for five different subsets of the first primary data set and the homogenized samples in the secondary data set. Severity is most significantly related toMEblue, the TPH2 SNP and the candidate FOXN1 gene in the combined male and homogenized female sub set. Homogenizing the second data set (which discarded three samples) also improved the MEblue and FOXN1 associations with severity.
  2. 1MEblue refers to the blue module eigengene, or first principal component of the blue module.
  3. 2SNP refers to the TPH2 SNP rs10784941.
  4. 3Here empiric replaces severity in cor(severity, FOXN1).