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Table 1 Univariate transcript heritability and linkage analysis compared to principal-component approach: chromosome 4q28.2-31.1 region

From: Comparison of strategies for identification of regulatory quantitative trait loci of transcript expression traits

Transcript Groupa Gene name Gene symbol H2 (SE)b H2 p-value LOD score Trait locus location Transcript gene locus
218935_at   EH-domain containing 3 EHD3 0.20 (0.13) 0.01 1.98 4q28.2 2p21
212652_s_at 1 sorting nexin 4 SNX4 0.21 (0.09) 0.001 3.03 4q28.2 3q21.2
212426_s_at 1 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide YWHAQ 0.40 (0.15) <0.001 2.12 4q28.2 2p25.1
207076_s_at 1 argininosuccinate synthetase ASS 0.19 (0.11) 0.01 1.17 4q28.2 9q34.1
213798_s_at 2 CAP, adenylate cyclase-associated protein 1 (yeast) CAP1 0.16 (0.09) 0.008 1.73 4q28.2 1p34.2
220143_at   LUC7-like (S. cerevisiae) LUC7L 0.16 (0.09) 0.013 1.79 4q28.3 16p13.3
204994_at 1 myxovirus (influenza virus) resistance 2 (mouse) MX2 0.30 (0.13) <0.001 3.72 4q28.3 21q22.3
200974_at   actin, alpha 2, smooth muscle, aorta ACTA2 0.20 (0.09) 0.003 1.61 4q28.3-q31.1 10q23.3
201397_at 2 phosphoglycerate dehydrogenase PHGDH 0.32 (0.12) <0.001 2.12 4q28.3-q31.1 1p12
203882_at 1 interferon-stimulated transcription factor 3, gamma 48 kDa ISGF3G 0.19 (0.10) 0.006 1.79 4q28.3-q31.1 14q11.2
203675_at 2 nucleobindin 2 NUCB2 0.47 (0.17) <0.001 3.15 4q28.3 11p15.1-p14
201195_s_at   solute carrier family 7, member 5 SLC7A5 0.16 (0.09) 0.01 1.59 4q31.1 16q24.3
201681_s_at 2 discs, large homolog 5 (Drosophila) DLG5 0.22 (0.12) 0.005 2.05 4q31.1 10q23
202531_at   interferon regulatory factor 1 IRF1 0.21 (0.14) 0.02 2.80 4q31.1 5q31.1
202732_at 2 protein kinase (cAMP-dependent, catalytic) inhibitor gamma PKIG 0.38 (0.11) <0.001 1.78 4q31.1 20q12-q13.1
Principal component analysis, 15 transcripts factorc N/A 0.29 (0.14) 0.001 1.99 4q28.3 N/A
   Group 1 factor 1 (loading MX2) N/A 0.27 (0.13) 0.002 2.28 4q28.3 N/A
   Group 1 factor 2 (loading YWHAQ) N/A 0.29 (0.13) 0.001 0.00 4q28.2-31.1 N/A
  1. aGroup 1 and 2 have transcripts correlated using bivariate analysis. Transcripts without correlation on bivariate analyses were not assigned a group.
  2. b H2, heritability; SE, standard error; N/A, not apply.
  3. c For principal component analysis, only factors with significant heritability (alpha = 0.05) are shown.