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Supplemental Material For SUPPLEMENTAL MATERIAL FOR Coexpression network based on natural variation in human gene expression reveals gene interactions and functions Renuka Nayak, Michael Kearns, Richard S. Spielman, Vivian G. Cheung Supplementary Figure 1 Supplementary Table 1. Gene pairs whose correlations in gene expression levels differ significantly (Pc<0.05) among the 3 datasets. Supplementary Table 2. Gene pairs that are correlated in gene expression levels with |R|>0.5 and are found within 500 kb of each other. Supplementary Table 3. Predicted functions of poorly characterized genes based on the functions of neighboring genes. Supplementary Figure 1. Genes identified in genome-wide association studies (grey) and their neighbors in the network. Red and green connections refer to positive and negative correlations, respectively. MICB has been implicated in AIDS progression (PMID: 19115949) TNF has been implicated in AIDS progression (PMID: 19115949) LTB has been implicated in AIDS progression (PMID: 19115949) ZNF224 has been implicated in Alzheimer's disease (PMID: 19118814) NDUFAB1 has been implicated in bipolar disorder (PMID: 17554300) SFRS10 has been implicated in body mass index (PMID: 19079260) and weight (PMID: 19079260) CTNNBL1 has been implicated in bone mineral density (PMID: 17903296) TGFBR3 has been implicated in bone mineral density (PMID: 19249006) IGF2R has been implicated in brain lesion load (PMID: 19010793) LSP1 has been implicated in breast cancer (PMID: 17529967) FBN1 has been implicated in breast cancer (PMID: 17903305) GLG1 has been implicated in breast cancer (PMID: 18463975) SCHIP1 has been implicated in Celiac disease (PMID: 18311140) RGS1 has been implicated in Celiac disease (PMID: 18311140) FADS2 has been implicated in Cholesterol (total) (PMID: 19060911), HDL cholesterol (PMID: 19060911, 19060906), LDL cholesterol (PMID: 19060911, 19060910), and triglycerides (PMID: 19060906). PSMA4 has been implicated in Chronic Obstructive Pulmonary Disease (PMID: 19300482), lung cancer (PMID: 18780872, 18385676, 18385738). SMAD7 has been implicated in colorectal cancer (PMID: 18372901, 18372905, 17934461) SMAD3 has been implicated in coronary disease (PMID: 17634449) CCR6 has been implicated in Crohn's disease (PMID: 18587394) STAT3 has been implicated in Crohn's disease (PMID: 18587394) BCL11A has been implicated in fetal hemoglobin levels (PMID: 18245381) and F-cell distribution (PMID: 17767159) CCND2 has been implicated in major depressive disorder (PMID: 19107115) SLC5A3 has been implicated in myocardial infarction (early onset) (PMID: 19198609) LDLR has been implicated in myocardial infarction (early onset) (PMID: 19198609), total cholesterol (PMID: 19060911) and LDL cholesterol (PMID: 19060911, 19060906, 19060910, 18193044, 18193043). ABI2 has been implicated in other subclinical atherosclerosis traits (PMID: 17903303) STAP1 (also known as BRDG1) has been implicated in Parkinson's disease (PMID: 17052657) SH2B3 has been implicated in Plasma eosinophil count (PMID: 19198610), Celiac disease (PMID: 18311140) and Type 1 diabetes (PMID: 17554300) POU2F1 has been implicated in plasma levels of liver enzymes (PMID: 18940312) HNF1B (also known as TCF2) has been implicated in prostate cancer (PMID: 17603485) STAT2 has been implicated in psoriasis (PMID: 19169254) TNFAIP3 has been implicated in psoriasis (PMID: 19169254), systemic lupus erythematosus (PMID: 18677312), and rheumatoid arthritis (PMID: 17982456, 17982456). KIF5A has been implicated in rheumatoid arthritis (PMID: 18794853) TNFRSF14 has been implicated in rheumatoid arthritis (PMID: 18794853) CD40 has been implicated in rheumatoid arthritis (PMID: 18794853) PLEK has been implicated in serum metabolites (PMID: 19043545) ICAM1 has been implicated in soluble ICAM-1 (PMID: 18604267, 18604267, 18604267) IMPA2 has been implicated in stroke (PMID: 17434096) BLK has been implicated in systemic lupus erythematosus (PMID: 18677312, 18204098) IRF5 has been implicated in systemic lupus erythematosus in women (PMID: 18204446) and Systemic lupus erythematosus (PMID: 18204098) TNPO3 has been implicated in systemic lupus erythematosus in women (PMID: 18204446) and systemic lupus erythematosus (PMID: 18204098) NCOA3 has been implicated in treatment response for acute lymphoblastic leukemia (PMID: 19176441) LMO4 has been implicated in treatment response to TNF antagonists (PMID: 18615156) BCL7B has been implicated in triglycerides (PMID: 18193044) TBL2 has been implicated in triglycerides (PMID: 18193044) PTPN1 has been implicated in Type 1 diabetes (PMID: 17554300) HLA-E has been implicated in Type 1 diabetes (PMID: 17632545) RAB5B has been implicated in Type 1 diabetes (PMID: 18198356) PTPN2 has been implicated in Type 1 diabetes (PMID: 18978792, 17554260) and Crohn's disease (PMID: 18587394, 17554300, 17554261) VEGFA has been implicated in Type 2 diabetes (PMID: 18372903) NOTCH2 has been implicated in Type 2 diabetes (PMID: 18372903) ADAMTS9 has been implicated in Type 2 diabetes (PMID: 18372903) MYC has been implicated in urinary bladder cancer (PMID: 18794855) Supplementary Table 1 Supplementary Table 1. Gene pairs whose correlations in gene expression levels differ significantly (Pc<0.05) among the 3 datasets Affy ID 1 Gene Symbol 1 Affy ID 2 Gene Symbol 2 R CEPH-Utah R ASN R YRI 200012_x_at RPL21 200026_at RPL34 0.53 0.88 0.86 200012_x_at RPL21 200029_at RPL19 0.42 0.88 0.80 200001_at CAPNS1 200041_s_at BAT1 -0.11 0.68 0.34 200001_at CAPNS1 200042_at C22orf28 0.28 -0.55 0.14 200008_s_at GDI2 200042_at C22orf28 0.62 -0.02 -0.11 200029_at RPL19 200042_at C22orf28 -0.41 0.40 -0.30 200023_s_at EIF3S5 200044_at SFRS9 -0.26 0.55 -0.27 200042_at C22orf28 200045_at ABCF1 0.64 -0.16 0.56 200036_s_at RPL10A 200046_at DAD1 0.30 -0.54 -0.01 200041_s_at BAT1 200046_at DAD1 -0.45 0.35 -0.33 200042_at C22orf28 200046_at DAD1 0.54 -0.48 -0.03 200042_at C22orf28 200052_s_at ILF2 0.61 -0.29 0.42 200001_at CAPNS1 200055_at TAF10 0.04 0.80 0.74 200003_s_at RPL28 200055_at TAF10 0.51 -0.25 0.01 200029_at RPL19 200055_at TAF10 0.61 -0.32 0.20 200034_s_at RPL6 200055_at TAF10 0.47 -0.39 0.09 200046_at DAD1 200055_at TAF10 -0.23 0.54 -0.34 200052_s_at ILF2 200055_at TAF10 -0.38 0.32 0.43 121_at PAX8 200056_s_at C1D 0.14 -0.60 -0.03 1861_at BAD 200059_s_at RHOA 0.47 -0.33 0.22 200016_x_at HNRPA1 200059_s_at RHOA -0.08 0.58 0.56 200029_at RPL19 200059_s_at RHOA -0.37 0.30 0.42 200042_at C22orf28 200059_s_at RHOA 0.55 -0.20 -0.34 200059_s_at RHOA 200063_s_at NPM1 -0.14 0.58 0.55 200055_at TAF10 200066_at IK 0.11 -0.63 -0.52 121_at PAX8 200071_at SMNDC1 0.08 -0.70 -0.37 200055_at TAF10 200071_at SMNDC1 -0.47 0.22 -0.64 121_at PAX8 200076_s_at C19orf50 -0.24 0.54 0.20 200059_s_at RHOA 200077_s_at OAZ1 -0.30 0.56 0.45 200059_s_at RHOA 200078_s_at ATP6V0B 0.45 -0.31 -0.27 1494_f_at CYP2A6 200079_s_at KARS -0.40 0.42 -0.06 200065_s_at ARF1 200079_s_at KARS 0.36 -0.49 -0.25 1494_f_at CYP2A6 200086_s_at COX4I1 -0.36 0.58 0.01 200042_at C22orf28 200086_s_at COX4I1 -0.21 0.61 0.21 200055_at TAF10 200086_s_at COX4I1 0.56 -0.47 -0.25 200019_s_at FAU 200088_x_at RPL12 0.80 0.25 0.62 200055_at TAF10 200089_s_at RPL4 0.59 -0.30 0.07 200028_s_at STARD7 200090_at FNTA -0.37 0.43 -0.22 200033_at DDX5 200094_s_at EEF2 -0.25 0.37 -0.58 200042_at C22orf28 200096_s_at ATP6V0E1 0.65 -0.40 0.22 200086_s_at COX4I1 200600_at MSN -0.03 -0.71 -0.20 121_at PAX8 200603_at PRKAR1A 0.19 -0.74 -0.01 1494_f_at CYP2A6 200603_at PRKAR1A 0.19 -0.64 -0.13 200079_s_at KARS 200619_at SF3B2 0.64 -0.14 0.41 200001_at CAPNS1 200623_s_at CALM3 0.04 0.71 0.55 200041_s_at BAT1 200623_s_at CALM3 0.34 0.83 0.66 200066_at IK 200623_s_at CALM3 0.14 -0.52 -0.56 121_at PAX8 200626_s_at MATR3 0.29 -0.74 -0.27 1494_f_at CYP2A6 200626_s_at MATR3 0.35 -0.61 -0.25 200008_s_at GDI2 200626_s_at MATR3 0.61 -0.10 -0.19 200035_at DULLARD 200626_s_at MATR3 -0.61 0.21 -0.39 200042_at C22orf28 200626_s_at MATR3 0.56 -0.52 0.21 200048_s_at JTB 200626_s_at MATR3 0.48 -0.18 -0.26 Page 1 Supplementary Table 1 200051_at SART1 200626_s_at MATR3 -0.68 -0.01 0.03 200055_at TAF10 200626_s_at MATR3 -0.60 0.33 -0.21 200070_at C2orf24 200626_s_at MATR3 -0.36 0.38 0.34 200073_s_at HNRPD 200626_s_at MATR3 -0.25 0.57 0.40 200055_at TAF10 200633_at UBB 0.27 -0.50 -0.26 200066_at IK 200634_at PFN1 0.26 -0.51 -0.54 200086_s_at COX4I1 200634_at PFN1 0.38 -0.49 -0.26 200005_at EIF3S7 200645_at GABARAP 0.48 -0.24 -0.16 200036_s_at RPL10A 200645_at GABARAP 0.44 -0.39 -0.14 200042_at C22orf28 200645_at GABARAP 0.36 -0.58 -0.17 200012_x_at RPL21 200650_s_at LDHA 0.38 0.86 0.68 200055_at TAF10 200650_s_at LDHA 0.41 -0.43 0.29 200029_at RPL19 200655_s_at CALM1 0.26 -0.51 -0.21 200046_at DAD1 200655_s_at CALM1 -0.35 0.56 -0.26 200079_s_at KARS 200655_s_at CALM1 0.08 -0.69 -0.03 200086_s_at COX4I1 200655_s_at CALM1 0.13 -0.64 -0.33 200096_s_at ATP6V0E1 200655_s_at CALM1 -0.50 0.49 -0.04 200626_s_at MATR3 200655_s_at CALM1 -0.45 0.53 0.05 200645_at GABARAP 200655_s_at CALM1 -0.43 0.40 0.20 200096_s_at ATP6V0E1 200657_at SLC25A5 0.44 -0.32 -0.37 200626_s_at MATR3 200657_at SLC25A5 0.51 -0.35 -0.28 200001_at CAPNS1 200668_s_at UBE2D3 0.09 -0.62 -0.51 200029_at RPL19 200668_s_at UBE2D3 -0.46 0.42 -0.19 200045_at ABCF1 200668_s_at UBE2D3 0.49 -0.13 -0.30 200046_at DAD1 200668_s_at UBE2D3 0.54 -0.56 0.27 200052_s_at ILF2 200668_s_at UBE2D3 0.66 -0.16 -0.02 200078_s_at ATP6V0B 200668_s_at UBE2D3 0.51 -0.35 0.04 200089_s_at RPL4 200668_s_at UBE2D3 -0.46 0.35 -0.01 200012_x_at RPL21 200674_s_at RPL32 0.59 0.92 0.80 200055_at TAF10 200674_s_at RPL32 0.54 -0.31 0.27 200041_s_at BAT1 200675_at CD81 -0.06
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