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Differential Gene Expression between
Han Chinese and Japanese
Yuan Yuan
Prof. Shuhua Xu’s group
Population genomic group
PICB
Chinese and Japanese are very similar in phenotype.
Expression variation among Chinese and Japanese individuals
Illumina's commercial whole genome expression array, Sentrix Human-6 Expression BeadChip version 2
These arrays utilize a bead pool with ~48,000 unique bead types
Each with several hundred thousand gene-specific 50mer probes attached.
Differently
expressed
Genome locations of 768 DE genes
Functional enrichment of 768 DE genes
Gene Ontology category
#Genes
a
cluster
Cellular metabolic process
391
RNA processing
50
Gene expression
213
RNA splicing
30
mRNA metabolic process
35
mRNA processing
31
Metabolic process
420
Nucleobase, nucleoside, nucleotide 225
and nucleic acid metabolic process
Protein folding
20
Cellular protein metabolic process
153
in #Other genesb
6812
470
3368
237
309
271
7717
3719
P-value for
c
enrichment
0.000
0.000
0.002
0.002
0.003
0.009
0.012
0.019
147
2385
0.034
0.043
Identify local (Cis) and distant (Trans) genetic regulators that
associate with gene expression difference
Population
Cis: # genes(snps)
Trans: # genes(snps)
CHB
39 (306)
271 (4544)
JPT
68 (648)
92 (1216)
10 15 20 25
−log2(pvalue)
CHB
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Gene
CTSS
PHB2
GCAT
GOLIM4
DPP7
MRPL54
PIGB
GMCL1
LIN52
DHRS4
DCAF10
P value
7.02E-07
3.11E-07
9.42E-08
2.67E-08
3.57E-07
2.70E-06
2.30E-06
5.78E-11
6.71E-08
4.68E-08
1.94E-06
CHB
JPT
expression expression
0.02
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-0.01
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0.02
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Cis
represented
SNP
rs12085336
rs11541468
rs5756825
rs7620923
rs13631
rs12459781
rs11071185
rs11126251
rs8006297
rs2332152
rs726363
2
R due to
Pvalue for
Pvalue for
genotype
association(CHB) association(JPT) variation
7.98E-10
7.54E-18
0.43
2.26E-09
3.23E-06
0.29
8.20E-06
1.62582E-05
0.29
9.54E-11
1.63E-06
0.28
1.07E-07
6.58E-06
0.27
1.96998E-05
1.16E-09
0.27
8.65E-06
1.64E-06
0.25
4.48919E-05
1.35157E-05
0.21
4.54423E-05
1.53141E-05
0.19
>1E-04
1.93953E-05
0.09
>1E-04
9.83721E-05
0.07
R due to
population
sepecific
genotype
effect
0.14
0.12
0.06
0.17
0.11
0.1
0.1
0.18
0.14
0.16
0.12
rs7412746
CHB
JPT
−0.15
−0.05
0.00
0.05
0.10
ENSG00000163131
37
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CC
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7
CT
10
TT
Melanoma
rs2224391
−0.10
−0.05
0.00
0.05
ENSG00000145982
CHB
JPT
44
51
AA
27
23
AC
8
7
CC
Height
rs6494537
−0.15
−0.10
0.00
0.00
0.10
0.10
ENSG00000074696
CHB
JPT
1
11
CC
28
27
CT
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43
TT
Hematological and biochemical tr aits
CTSS vs cis-SNPs
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1.0
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2.0
3.0
CHB
150000000
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150500000
151000000
151500000
Position on Chr1
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150000000
150500000
151000000
Position on Chr1
151500000
Dr. Shuhua Xu
Yang ling, Lu dongsheng, Shi meng, Lou haiyi
Jin wenfei, Pankaj
All in population genomics group