5 CONCLUSIONS AND DISCUSSION
5.2 D ISCUSSION
If All SNPs put into gene-gene interaction test, the number of test is too many. In signal-SNP association test between SNP genotypes and case-control status, it only discoveries significant SNPs with disease and neglect Some SNPs are weakly related with disease, but affected disease after combining with other SNPs. So we use the properties of endophenotype to find these significant SNPs weakly associated with disease from association test between gene expression of each probe set and all SNP genotypes. We collect these significant SNPs from single-SNP association test of case-control and continuous outcome (gene expression) and then do gene-gene interaction to add more opportunity for searching possible underlying disease genes.
But there is a problem, what criteria of PHE judging the expression value of probe sets as an endophenotype is appropriate. In the future, we will keep on overcoming this problem and utilize the real SNP data that provided by Moffatt et al [5] to confirm the assumption.
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Figure 1 A surrogate endpoint versus an endophenotype in the disease process.
Figure 2 The confidence interval of PHEs on all chromosomes (red: PHE, blue: the low bound of PHE). | a. the confidence interval of total PHEs, b. the confidence interval of the low bound of PHEs >0
Figure 3 The density plot of PHEs. | a. Density plot of total PHEs. b. Density plot of PHEs >0. c. Density plot of PHEs with unadjusted p-value <0.05. d. Density plot with q-value<0.05.
Figure 4 The scatter plot of heritability versus total PHEs.
a. Scatter plot with a smooth line of loss function.
b. Scatter plot with a regression line.
Figure 5 The scatter plot of heritability versus PHEs >0.
a. Scatter plot with a smooth line of loss function.
b. Scatter plot with a regression line.
Figure 6 The scatter plot of heritability versus PHEs with unadjusted p-value <0.05.
a. Scatter plot with a smooth line of loss function.
b. Scatter plot with a regression line.
Figure 7 The scatter plot of heritability versus PHEs with q-value <0.05.
a. Scatter plot with a smooth line of loss function.
b. Scatter plot with a regression line.
Figure 8 The bar-plot of proportion of probe sets with max significant SNPs’ LOD
>6 versus PHEs.
a. The bar-plot of proportion of probe sets with max significant SNPs’ LOD >6 versus total PHEs.
b. The bar-plot of proportion of probe sets with max significant SNPs’ LOD >6 versus PHEs >0.
c. The bar-plot of proportion of probe sets with max significant SNPs’ LOD >6 versus PHEs with
Figure 9 The bar-plot of the number (cis eSNPs <100kb) versus PHEs.
a. The bar-plot of the number versus total PHEs.
b. The bar-plot of the number versus PHEs>0.
c. The bar-plot of the number versus PHEs with unadjusted p-value <0.05.
Figure 10 The bar-plot of the number (cis eSNPs >100kb) versus PHEs.
a. The bar-plot of the number versus total PHEs.
b. The bar-plot of the number versus PHEs>0.
c. The bar-plot of the number versus PHEs with unadjusted p-value <0.05.
Figure 11 The bar-plot of the number (trans) versus PHEs.
a. The bar-plot of the number versus total PHEs.
b. The bar-plot of the number versus PHEs>0.
c. The bar-plot of the number versus PHEs with unadjusted p-value <0.05.
Figure 12 The bar-plot of the number (cis eSNPs <100 kb) versus heritability and differential expression.
a. The bar-plot of the number versus heritability and differential expression for probe sets with total PHEs.
b. The bar-plot of the number versus heritability and differential expression for probe sets with PHEs>0.
c. The bar-plot of the number versus heritability and differential expression for probe sets with PHEs with unadjusted p-value <0.05.
Figure 13 The bar-plot of the number (cis eSNPs >100 kb) versus heritability and differential expression.
a. The bar-plot of the number versus heritability and differential expression for probe sets with total PHEs.
b. The bar-plot of the number versus heritability and differential expression for probe sets with PHEs>0.
c. The bar-plot of the number versus heritability and differential expression for probe sets with PHEs with unadjusted p-value <0.05.
Figure 14 The bar-plot of the number (trans) versus heritability and differential expression.
a. The bar-plot of the number versus heritability and differential expression for probe sets with total PHEs.
b. The bar-plot of the number versus heritability and differential expression for probe sets with PHEs>0.
c. The bar-plot of the number versus heritability and differential expression for probe sets with PHEs with unadjusted p-value <0.05.
Figure 15 The density plot of LOD score for cis eSNPs <100 kb (red), cis eSNPs >100 kb (green) and trans (trans) between X-limit (3, 50) and Y-limit (0, 0.8) for probe sets with total PHEs.
a. The density plot of LOD score for cis eSNPs <100 kb.
b. The density plot of LOD score for cis eSNPs >100 kb.
c. The density plot of LOD score for trans.
d. The density plot of LOD score for cis eSNPs <100 kb, cis eSNPs >100 kb and trans.
Figure 16 The density plot of LOD score for cis eSNPs <100 kb (red), cis eSNPs >100 kb (green) and trans (blue) between X-limit (3, 25) and Y-limit (0, 0.3) for probe sets with total PHEs.
a. The density plot of LOD score for cis eSNPs <100 kb.
b. The density plot of LOD score for cis eSNPs >100 kb.
c. The density plot of LOD score for trans.
d. The density plot of LOD score for cis eSNPs <100 kb, cis eSNPs >100 kb and trans.
Figure 17 The density plot of LOD score for cis eSNPs <100 kb (red), cis eSNPs >100 kb (green) and trans (blue) between X-limit (3, 50) and Y-limit (0, 0.8) for probe sets with PHEs>0.
a. The density plot of LOD score for cis eSNPs <100 kb.
b. The density plot of LOD score for cis eSNPs >100 kb.
c. The density plot of LOD score for trans.
d. The density plot of LOD score for cis eSNPs <100 kb, cis eSNPs >100 kb and trans.
Figure 18 The density plot of LOD score for cis eSNPs <100 kb (red), cis eSNPs >100 kb (blue) and trans (blue) between X-limit (3, 25) and Y-limit (0, 0.5) for probe sets with PHEs>0.
a. The density plot of LOD score for cis eSNPs <100 kb.
b. The density plot of LOD score for cis eSNPs >100 kb.
c. The density plot of LOD score for trans.
d. The density plot of LOD score for cis eSNPs <100 kb, cis eSNPs >100 kb and trans.
Figure 19 The density plot of LOD score for cis eSNPs <100 kb (red), cis eSNPs >100 kb (green) and trans (blue) between X-limit (3, 50) and Y-limit (0, 0.8) for probe sets with PHEs with unadjusted p-value <0.05.
a. The density plot of LOD score for cis eSNPs <100 kb.
b. The density plot of LOD score for cis eSNPs >100 kb.
c. The density plot of LOD score for trans.
d. The density plot of LOD score for cis eSNPs <100 kb, cis eSNPs >100 kb and trans.
Figure 20 The density plot of LOD score for cis eSNPs <100 kb (red), cis eSNPs >100 kb (green) and trans (blue) between X-limit (3, 25) and Y-limit (0, 0.5) for probe sets with PHEs with unadjusted p-value <0.05.
a. The density plot of LOD score for cis eSNPs <100 kb.
b. The density plot of LOD score for cis eSNPs >100 kb.
c. The density plot of LOD score for trans.
d. The density plot of LOD score for cis eSNPs <100 kb, cis eSNPs >100 kb and trans.
Figure 21 The density plot of LOD score for cis eSNPs <100 kb (red), cis eSNPs >100 kb (green) and trans (blue) between X-limit (3, 10) and Y-limit (0, 0.8) for probe sets with PHEs with q-value <0.05.
a. The density plot of LOD score for cis eSNPs <100 kb.
b. The density plot of LOD score for cis eSNPs >100 kb.
c. The density plot of LOD score for trans.
d. The density plot of LOD score for cis eSNPs <100 kb, cis eSNPs >100 kb and trans.
Table 5 The PHEs of probe sets with q-value < 0.05.
ProbeID low PHE chr Start End q-value
223949_at 0.210989 0.291867 21 42675053 42689269 1.54E-05
223952_x_at 0.14619 0.210583 2 1.7E+08 1.7E+08 0.000156
238076_at 0.18335 0.264808 1 1.51E+08 1.51E+08 0.000156
203627_at 0.176716 0.258253 15 97010284 97320636 0.000248
226841_at 0.127579 0.192336 11 58732558 58734705 0.001084
235835_at 0.153614 0.232668 19 63631810 63651932 0.00113
239938_x_at 0.131783 0.202743 5 88066154 88066571 0.001813
209772_s_at 0.101687 0.157232 24 19542359 19542777 0.001813
220177_s_at 0.100664 0.156129 21 42665067 42689269 0.001813
209071_s_at 0.128678 0.19985 1 1.6E+08 1.6E+08 0.001813
214254_at 0.150264 0.23343 23 1.51E+08 1.51E+08 0.001813
65472_at 0.151357 0.235664 2 85744034 85745751 0.001813
218390_s_at 0.148063 0.230837 10 1.2E+08 1.2E+08 0.001813
219799_s_at 0.130186 0.206607 2 1.7E+08 1.7E+08 0.003115
239199_at 0.145202 0.230571 17 579571 580102 0.003115
1570156_s_at 0.132495 0.211029 15 30849385 30850684 0.003243
202615_at 0.10535 0.169551 9 77562838 77875925 0.004321
222842_at 0.132372 0.214778 1 35942865 35991660 0.005079
1553296_at 0.093781 0.152233 3 1.02E+08 1.02E+08 0.005079
1552514_at 0.11781 0.192029 22 40719270 40748979 0.005473
1562098_at 0.120392 0.199272 12 98922496 98923786 0.008119
223948_s_at 0.101249 0.168402 21 42675053 42689269 0.00885
1570087_at 0.186288 0.315897 22 41759088 41772869 0.013429
239904_at 0.113997 0.193411 6 83136598 83137111 0.013429
239786_at 0.125965 0.214028 3 1.39E+08 1.39E+08 0.013429
226997_at 0.108961 0.18607 2 30775651 30778742 0.014572
242477_at 0.116073 0.198662 9 44414427 44415310 0.014812
238676_at 0.117222 0.203013 1 52266829 52267579 0.018643
226818_at 0.075209 0.130817 18 26899939 26901242 0.019778
266_s_at 0.063488 0.110892 24 19540661 19542776 0.020873
244783_at 0.098588 0.175553 9 1.01E+08 1.01E+08 0.029632
235667_at 0.098162 0.175046 10 15595956 15596395 0.029632
204837_at 0.107754 0.193471 9 6522466 6635650 0.03267
230282_at 0.095278 0.172182 16 79644602 79645066 0.035667
242142_at 0.105077 0.190967 6 1.14E+08 1.14E+08 0.03723
219067_s_at -0.17093 -0.05114 15 73122679 73129132 0.040256
240089_at 0.104381 0.192788 4 1.21E+08 1.21E+08 0.04628
Table 6 The probe sets with PHEs > 0.2.
65472_at 0.2357 0.0026 0.1514 2
224459_at 0.2341 0.0148 0.0342 14
214254_at 0.2334 0.0026 0.1503 23
235835_at 0.2327 0.0023 0.1536 19
218390_s_at 0.2308 0.0025 0.1481 10
239199_at 0.2306 0.0027 0.1452 17
1570156_s_at 0.2110 0.0023 0.1325 15
223952_x_at 0.2106 0.0015 0.1462 2
1563113_at 0.2069 0.0077 0.0623 1
219799_s_at 0.2066 0.0022 0.1302 2
1556538_at 0.2038 0.0134 0.0131 3
238676_at 0.2030 0.0027 0.1172 21
239938_x_at 0.2027 0.0019 0.1318 5
1557548_at 0.2018 0.0073 0.0614 10
Table 7 Genes of significant SNPs (LOD>6) overlap with asthma or atopy genes
SNP chr LOD Gene
rs2844484 6 6.146 LTA
rs2239704 6 6.403 LTA
rs1041981 6 7.141 LTA
rs10776482 4 7.124 TLR10
rs4129009 4 13.141 TLR10
rs10776483 4 7.144 TLR10 rs11096955 4 6.049 TLR10 rs11096956 4 9.563 TLR10
rs3024498 1 8.219 IL10
rs3024496 1 7.823 IL10
rs1518111 1 9.300 IL10
rs3024490 1 7.265 IL10
rs1800872 1 8.131 IL10
rs1800896 1 7.473 IL10
Table 8 The probe set with max eSNPs' LOD >6 (PHEs with q-value < 0.05).
Table 9 Cis eSNPs < 100 kb (PHEs with q-value < 0.05).
Table 10 Cis eSNPs > 100 kb (PHEs with q-value <0.05).
probe set ID PHE hertibility q-value(SAM) chr cis eSNPs
<100kb
Appendix I
Appendix II
25 genes that have been associated with asthma or atopy phenotype in >6 populations
Gene Related Gene
HLA-DRB1 TNF IFNG RA MYLK MLCK HLA-DPB1 DRB1 HLA-A LOC642072 HLA-B HLA-C INFRSF10A INFRSF10B LTC4S ALOX5 LTA4H STK32C GSTA1 MGST2 YWHAZ CYSLTR1 GSTA2 CYSLTR2
SEC23IP PGCP
Asthma genes (review papers from 2003, 2006, 2008)
AACT(SERPINA3) CCL11 CMA1 DCNP1 GATA3 HLA IL15 IL5RA MRP1 PTGER3 TBXA2R VDR
ACE CCL2 COX2 DEFB1 GCLM HNMT IL16 IL8 MUC7 PTGIR TCRA/D
ACP1 CCL24 CRHR1 DPP10 GPRPA ICOS IL17F IL8RA NAT2 RANTES TGFB1
ADAM33 CCL26 CRTH2 ECP GSTM1 IFNG IL18 IRF1 NOD1 SCCE TGFB2
ADRB2 CCL5 CSF2 EDN1 GSTP1 IFNGR1 IL1A IRF2 NOS1 SDF1 TIMP1
AGT CCR3 CSTA EDNRA GSTT1 IFNGR2 IL1B ITGB3 NOS2A SELP TLR10
AICDA CCR5 CTLA4 EOTAXIN1 HAVCR1 IGHG IL1RL1 KCNS3 NOS3 SOCS1 TLR2
ALOX5 CD14 CXCL12 EOTAXIN2 HAVCR2 IKAP IL1RN LTA ORMDL3 SPINK5 TLR4
CHIA CD40 CXCR3 EP2 HLADPB1 IL10 IL27 LTA PAFAH STAT3 TLR6
C3 CD86 CYFIP2 FCER1B HLA-DQA1 IL12B IL3 LTC4S PGDS STAT4 TLR9
C3AR1 CFTR CYSLTR1 FCER2 HLA-DQB1 IL12RB1 IL4 MCP1 PHF11 STAT6 TNF
C5 CHRM3 CYSLTR2 FLAP HLADRB1 IL13 IL4RA MIF PTGDR TAP1 UGRP1
CC16/CC10 CLCA1 DAP3 FLG HLA-G IL13RA1 IL5 MMP9 PTGER2 TBX21 VCAM1
NOS1 CALM3 CALM1 NOS3 NOS2A NANOS1 CALM2 TNF
CCL5 EEF1A1 CCR5 CCL2 CCL4L1 CCR2 CCL4L2 CCL3 CXCL9 IFNG
TRIM24 CXCL10 CCL4 TNF
SPINK5 NETS KLK6 PLG DSG1 KLK1 KLK5 SPINK5L3 DSP SERPINA13
KLK7 DSG3
STAT6 JUN STK32C IL5 IL10 IL4 CD4 IL13 CD8A IFNG FAM48A TNF
TBXA2R PTGER4 PTGER3 STK32C SAC YWHAZ PTGIR PTGER1 PTGS2 PTGDS
ADCY7 INS SEC23IP
TGFB1 PLAT PLG NUDT6 IL10 C20orf181 IL4 FGF13 IFNG TNF
FGF2
TNF IL1A MAPK14 IL10 IL4 IL1B IFNG MAPK1 AHSA1 CC16/CC10 PLA2G4A TFF1 STK32C YWHAZ TFF2 SFTPB SFTPA2 SEC23IP TFF3
SFTPC
HLA-DQB1 HLA-DQA1 DRB1 IDDM2 IDDM1 HLA-DRB1 INS HLA-DPB1 RA
GRPA(AAA1) PSORS# DNAH8 KRT5 HLA-DRB4 SLC7A10 SLC3A2 ATP5E SLC36A1 KRT19 PSORS1 KRT14 HLA-C GJA8 CALM2 GSTM1 SLC45A2 GSTP1 GSTM2 GSR GSPT2 GSPT1 CYP1A2 CYP1A1
GSTP1 CYP1A2 CYP1A1 G6PD XDH GSTA1 GSR EPHX1 CAT GSTA2