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Status
Public on May 08, 2008
Title
Evaluation of Genetic Variation Contributing to Differences in Gene Expression between Populations
Organism
Homo sapiens
Experiment type
Expression profiling by array
Summary
Gene expression is a complex quantitative trait partially regulated by genetic variation in DNA sequence. Population differences in gene expression could contribute to some of the observed differences in susceptibility to common diseases and responses to drug treatments. We characterize gene expression in the full set of HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry for 9,156 transcript clusters (gene-level) evaluated using the Affymetrix GeneChip® Human Exon 1.0 ST Array. Gene expression was found to differ significantly between these samples for 383 transcript clusters. Biological processes including ribosome biogenesis and antimicrobial humoral response were found to be enriched in these differential genes, suggesting their possible roles in contributing to the population differences at a higher level than mRNA expression and the population differences in response to environmental information. Genome-wide association studies for local or distant genetic variants that correlate with the differentially expressed genes enabled identification of significant associations with one or more single nucleotide polymorphisms (SNPs), consistent with the hypothesis that genetic factors and not simply population identity or other characteristics (age of cell lines, length of culture etc.) contribute to differences in gene expression in these samples. Our results provided a comprehensive view of the genes differentially expressed between populations and the enriched biological processes involved in these genes. We also provided an evaluation of the contribution of genetic variation and non-genetic factors to the population differences in gene expression. Keywords: exon array
Overall design
Gene expression on 176 HapMap cell lines.
Contributor(s)
Zhang W , Duan S , Kistner EO , Bleibel WK , Huang RS , Clark TA , Chen TX , Schweitzer AC , Blume JE , Cox NJ , Dolan ME
Citation(s)
18313023 , 19925429 , 19164090 , 18439551 , 19795565
Submission date
May 18, 2007
Last update date
Aug 20, 2019
Contact name
Eileen Dolan
E-mail(s)
edolan@medicine.bsd.uchicago.edu
Phone
773-702-4441
Fax
773-702-0963
Organization name
University of Chicago
Department
Medicine
Lab
Dolan Lab
Street address
5841 S. Maryland
City
Chicago
State/province
IL
ZIP/Postal code
60657
Country
USA
Platforms (1)
GPL5175
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
Samples (176)
Relations
BioProject
PRJNA99987
383 population differentially expressed transcript clusters header descriptions
ID_REF
transcript cluster
GSM188687
GM06985
GSM188775
GM06991
GSM188786
GM06993
GSM188797
GM06994
GSM188808
GM07000
GSM188819
GM07019
GSM188830
GM07022
GSM188841
GM07029
GSM188852
GM07034
GSM188688
GM07048
GSM188699
GM07055
GSM188710
GM07056
GSM188721
GM07345
GSM188732
GM07348
GSM188743
GM07357
GSM188754
GM10830
GSM188765
GM10831
GSM188773
GM10835
GSM188774
GM10838
GSM188776
GM10839
GSM188777
GM10846
GSM188778
GM10847
GSM188779
GM10851
GSM188780
GM10854
GSM188781
GM10856
GSM188782
GM10857
GSM188783
GM10859
GSM188784
GM10860
GSM188785
GM10861
GSM188787
GM10863
GSM188788
GM11829
GSM188789
GM11830
GSM188790
GM11831
GSM188791
GM11832
GSM188792
GM11839
GSM188793
GM11840
GSM188794
GM11881
GSM188795
GM11882
GSM188796
GM11992
GSM188798
GM11993
GSM188799
GM11994
GSM188800
GM11995
GSM188801
GM12003
GSM188802
GM12004
GSM188803
GM12005
GSM188804
GM12006
GSM188805
GM12043
GSM188806
GM12044
GSM188807
GM12056
GSM188809
GM12057
GSM188810
GM12144
GSM188811
GM12145
GSM188812
GM12146
GSM188813
GM12154
GSM188814
GM12155
GSM188815
GM12156
GSM188816
GM12234
GSM188817
GM12239
GSM188818
GM12248
GSM188820
GM12249
GSM188821
GM12264
GSM188822
GM12707
GSM188823
GM12717
GSM188824
GM12740
GSM188825
GM12750
GSM188826
GM12751
GSM188827
GM12752
GSM188828
GM12753
GSM188829
GM12760
GSM188831
GM12761
GSM188832
GM12762
GSM188833
GM12763
GSM188834
GM12801
GSM188835
GM12802
GSM188836
GM12812
GSM188837
GM12813
GSM188838
GM12814
GSM188839
GM12815
GSM188840
GM12864
GSM188842
GM12865
GSM188843
GM12872
GSM188844
GM12873
GSM188845
GM12874
GSM188846
GM12875
GSM188847
GM12878
GSM188848
GM12891
GSM188849
GM12892
GSM188850
GM18500
GSM188851
GM18501
GSM188853
GM18502
GSM188854
GM18503
GSM188855
GM18504
GSM188856
GM18505
GSM188857
GM18506
GSM188858
GM18507
GSM188859
GM18508
GSM188860
GM18515
GSM188861
GM18516
GSM188862
GM18517
GSM188689
GM18521
GSM188690
GM18522
GSM188691
GM18523
GSM188692
GM18852
GSM188693
GM18853
GSM188694
GM18854
GSM188695
GM18855
GSM188696
GM18856
GSM188697
GM18857
GSM188698
GM18858
GSM188700
GM18859
GSM188701
GM18860
GSM188702
GM18861
GSM188703
GM18862
GSM188704
GM18863
GSM188705
GM18870
GSM188706
GM18872
GSM188707
GM18912
GSM188708
GM18913
GSM188709
GM18914
GSM188711
GM19092
GSM188712
GM19093
GSM188713
GM19094
GSM188714
GM19098
GSM188715
GM19099
GSM188716
GM19100
GSM188717
GM19101
GSM188718
GM19102
GSM188719
GM19103
GSM188720
GM19116
GSM188722
GM19119
GSM188723
GM19120
GSM188724
GM19127
GSM188725
GM19128
GSM188726
GM19129
GSM188727
GM19130
GSM188728
GM19131
GSM188729
GM19132
GSM188730
GM19137
GSM188731
GM19138
GSM188733
GM19139
GSM188734
GM19140
GSM188735
GM19141
GSM188736
GM19142
GSM188737
GM19143
GSM188738
GM19144
GSM188739
GM19145
GSM188740
GM19152
GSM188741
GM19153
GSM188742
GM19154
GSM188744
GM19159
GSM188745
GM19160
GSM188746
GM19161
GSM188747
GM19171
GSM188748
GM19172
GSM188749
GM19173
GSM188750
GM19192
GSM188751
GM19193
GSM188752
GM19194
GSM188753
GM19200
GSM188755
GM19201
GSM188756
GM19202
GSM188757
GM19203
GSM188758
GM19204
GSM188759
GM19205
GSM188760
GM19206
GSM188761
GM19207
GSM188762
GM19208
GSM188763
GM19209
GSM188764
GM19210
GSM188766
GM19211
GSM188767
GM19221
GSM188768
GM19222
GSM188769
GM19223
GSM188770
GM19238
GSM188771
GM19239
GSM188772
GM19240
Data table
ID_REF
GSM188687
GSM188775
GSM188786
GSM188797
GSM188808
GSM188819
GSM188830
GSM188841
GSM188852
GSM188688
GSM188699
GSM188710
GSM188721
GSM188732
GSM188743
GSM188754
GSM188765
GSM188773
GSM188774
GSM188776
GSM188777
GSM188778
GSM188779
GSM188780
GSM188781
GSM188782
GSM188783
GSM188784
GSM188785
GSM188787
GSM188788
GSM188789
GSM188790
GSM188791
GSM188792
GSM188793
GSM188794
GSM188795
GSM188796
GSM188798
GSM188799
GSM188800
GSM188801
GSM188802
GSM188803
GSM188804
GSM188805
GSM188806
GSM188807
GSM188809
GSM188810
GSM188811
GSM188812
GSM188813
GSM188814
GSM188815
GSM188816
GSM188817
GSM188818
GSM188820
GSM188821
GSM188822
GSM188823
GSM188824
GSM188825
GSM188826
GSM188827
GSM188828
GSM188829
GSM188831
GSM188832
GSM188833
GSM188834
GSM188835
GSM188836
GSM188837
GSM188838
GSM188839
GSM188840
GSM188842
GSM188843
GSM188844
GSM188845
GSM188846
GSM188847
GSM188848
GSM188849
GSM188850
GSM188851
GSM188853
GSM188854
GSM188855
GSM188856
GSM188857
GSM188858
GSM188859
GSM188860
GSM188861
GSM188862
GSM188689
GSM188690
GSM188691
GSM188692
GSM188693
GSM188694
GSM188695
GSM188696
GSM188697
GSM188698
GSM188700
GSM188701
GSM188702
GSM188703
GSM188704
GSM188705
GSM188706
GSM188707
GSM188708
GSM188709
GSM188711
GSM188712
GSM188713
GSM188714
GSM188715
GSM188716
GSM188717
GSM188718
GSM188719
GSM188720
GSM188722
GSM188723
GSM188724
GSM188725
GSM188726
GSM188727
GSM188728
GSM188729
GSM188730
GSM188731
GSM188733
GSM188734
GSM188735
GSM188736
GSM188737
GSM188738
GSM188739
GSM188740
GSM188741
GSM188742
GSM188744
GSM188745
GSM188746
GSM188747
GSM188748
GSM188749
GSM188750
GSM188751
GSM188752
GSM188753
GSM188755
GSM188756
GSM188757
GSM188758
GSM188759
GSM188760
GSM188761
GSM188762
GSM188763
GSM188764
GSM188766
GSM188767
GSM188768
GSM188769
GSM188770
GSM188771
GSM188772
3026969
7.631383894
6.980895117
7.256016054
7.07080755
6.323528317
7.002752318
7.10522093
7.264076609
6.984825895
7.198849835
7.317946205
6.980895117
6.826264742
7.233653313
7.134867677
7.123796205
7.056721089
7.183266016
7.001001993
7.169925001
7.208655935
6.929503252
7.127337883
7.254225533
7.415927017
7.235887744
7.226059329
7.466316809
7.502287163
7.129994879
6.658724078
7.287840772
6.962136231
7.463133825
7.340008117
7.192613824
7.341810732
7.295023681
7.065082672
7.095062037
7.3242458
7.171258412
6.903476795
7.319745777
7.172147438
7.349474588
7.012384509
7.292329614
7.216685127
7.386051108
6.936455699
6.964751608
7.208210027
7.267660759
7.336854137
7.154823813
7.072129112
7.258702322
7.358045318
7.099036131
7.354435917
6.913445126
7.304008023
7.306255095
7.151717217
7.438149141
7.328297153
7.358045318
7.092854834
7.055401442
7.284699531
7.165037149
7.343613592
7.182376138
7.214900396
6.554255104
7.024656825
6.762504881
6.967803761
6.93384794
6.717438768
7.116273882
6.879250583
7.242146336
7.418646205
7.220701746
7.225166233
6.82025378
6.932978845
6.847765946
7.22471971
6.549278381
6.941673342
6.86543563
6.717862757
6.431327116
7.255568399
7.059800904
6.764210319
7.016327578
7.00494065
6.894384544
7.145063084
7.127337883
6.333138942
7.409584307
7.067284184
6.85810497
6.548034752
6.962572079
7.184155961
7.444504741
6.4549945
6.818108007
7.188606706
7.02641121
7.059360876
6.933413383
6.900878104
6.990506418
7.08667705
7.164148672
6.649051333
6.580856925
6.840879892
7.494994937
6.686548254
6.735690404
7.243487881
6.749299573
7.127780672
6.996627507
6.497649509
6.984389065
6.661670385
7.209101859
7.390121277
6.956907573
6.844322254
7.098594494
7.234100166
7.1770383
6.980895117
6.759947377
7.13841286
7.294125595
7.113620163
7.137526459
7.069045722
6.725498376
6.55466999
6.897847212
6.617176945
6.822400079
6.616339979
7.100361151
7.173481104
6.976529408
6.606721677
6.97783892
6.762504881
6.92776593
7.073010244
6.728469731
7.217577593
7.333250514
7.192613824
6.824117497
7.135310764
6.900012035
6.96998445
6.586272541
6.817678916
7.403244491
7.054961597
6.905642923
3026988
8.582507384
8.476792668
8.551378599
8.364304361
9.372258169
8.44242887
8.423831548
8.570531276
8.810356375
8.161461559
8.581070021
8.598801836
9.152152987
8.316297536
8.607911016
8.114301865
8.389528896
8.765539652
8.542285035
8.417158435
8.246577547
8.371441115
8.503068797
8.526975374
8.505936628
8.56191118
8.450539023
8.195946029
8.250840833
8.694328516
8.667900488
8.247998565
8.634293513
8.277383566
8.355742635
8.694809207
8.318197211
8.142114866
7.416380178
8.867294555
8.247051211
8.313448272
8.806981261
8.503068797
8.564784293
8.843158283
7.390573593
8.497333925
8.303478196
8.686157758
8.634293513
8.483956671
8.595925766
8.709232913
8.595446445
8.409057406
8.32674738
8.658775391
8.68039129
8.279280498
8.352413778
8.333874552
8.461992369
8.548506671
8.546113592
8.255578637
8.615583814
8.879851097
8.498289664
8.706828562
8.74916821
8.386196078
8.139756574
8.684716053
8.854259173
8.117600009
7.919163051
8.530323736
8.786254861
8.590653614
8.132211599
8.431936642
9.145836182
8.713080205
8.418111644
8.875504165
8.934951646
9.393242854
9.229476124
8.982375812
8.66309751
8.956237718
9.321048438
8.938821056
9.003200564
9.293268282
8.893377823
9.099214113
8.826271545
8.770356136
9.152638929
9.004169393
8.701058772
8.827236308
8.835437741
8.798785775
8.312973423
8.965916671
8.999325454
8.986249445
8.991576244
8.420971457
9.289370426
8.910775814
8.878885072
9.172566582
9.226556168
8.691925158
9.040515495
8.940755892
8.725586709
8.742429108
9.082712904
9.496320115
9.24748608
8.827718698
8.205402188
9.076405131
8.920444488
8.826271545
8.560474718
9.208553372
9.192502088
8.884681561
8.653013397
8.846053871
8.710194698
8.513585458
8.661656744
8.875504165
8.908358993
8.995935009
8.775654974
8.859569377
9.001262967
8.957205516
8.696251318
8.723662353
9.014827898
8.598322473
9.035667673
9.177914366
8.961560876
8.547070802
8.735691228
9.280114128
9.040030689
9.178886751
8.651573047
8.609829052
8.852328363
8.368586198
8.433844045
8.704424371
9.23823696
8.768429469
9.068157776
9.0002942
8.934951646
8.807945549
8.014638749
9.416676404
8.867294555
8.855224613
8.87791907
9.287421602
2757347
7.380626104
7.108756668
7.242593502
7.376106922
6.798819855
7.201969077
7.328297153
7.353533719
6.967367681
7.131323614
7.379270191
7.377010638
6.929068892
7.102569874
7.342261424
7.214900396
7.180596587
6.830131106
6.932978845
6.759521202
7.320645657
7.007567272
6.871045431
7.216238919
7.21400813
7.208655935
7.178817307
7.048366119
7.214900396
7.218470125
7.35398481
7.164148672
7.352631583
6.993129285
7.248855533
7.226059329
7.063761984
7.156599391
6.858536021
7.29592183
7.100361151
7.297718319
6.987447274
7.095062037
7.184155961
7.209101859
7.062001321
7.422725979
7.06244146
7.330998754
7.48861718
7.195285996
7.260941325
7.351278493
7.039578597
6.961264594
7.031237309
7.624950018
7.056721089
7.121140685
7.146837138
7.341360055
7.242146336
7.042214078
7.192168521
7.022902738
7.062001321
7.266764625
7.062881616
7.265420544
7.160151374
7.025095393
6.670937554
7.010194573
6.996190163
7.109198715
7.073450837
7.132209525
7.0611211
6.834858964
6.763357556
6.705576162
6.71447147
7.042214078
7.001001993
7.051443494
7.178817307
6.733566012
6.841740358
6.894384544
6.633516635
6.843461539
7.076094778
6.55798996
6.637292405
6.887463083
7.029920877
6.725498376
6.773596441
7.008005108
6.982205204
7.393740223
7.137526459
7.297269173
6.901311169
7.0580409
6.69415392
7.012822553
6.901311169
6.682326065
6.86026043
7.170369454
7.210885724
7.338656319
6.863278937
6.691195288
7.077857767
6.784275196
7.459042447
7.0611211
7.240804939
7.034748614
6.955600845
7.102128094
6.670937554
6.980895117
6.731017473
7.11671623
7.106546699
7.099477787
6.717014801
6.820682997
6.638971132
6.756112593
6.755686615
7.173481104
7.258702322
7.091972078
6.986136498
6.965187572
7.015889384
7.27034955
6.794539446
7.115389238
7.162816084
7.064642424
6.770182091
7.016327578
6.812960305
6.870613785
6.86586703
6.757816723
7.054081961
6.885733527
6.841310114
7.129109143
6.773596441
7.006691656
6.813389164
6.83142027
7.088882997
6.684859105
7.087559375
7.080943695
7.356691678
7.083148471
7.200186552
7.103453488
7.058920865
6.797535508
6.726771681
6.557574878
6.939498981
7.099477787
6.804816008
6.69880544
3442427
8.930115376
9.541316779
9.225096252
8.875021201
9.378113606
9.332261878
8.748686805
9.358597775
8.622778638
9.016281526
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Total number of rows: 383 Table truncated, full table size 785 Kbytes .
Supplementary file
Size
Download
File type/resource
GSE7851_LCL-cell-line-and-characteristics.txt
6.8 Kb
(ftp) (http)
TXT
GSE7851_RAW.tar
6.5 Gb
(http) (custom)
TAR (of CEL)
GSE7851_mask-probeset-ge2.txt
922.2 Kb
(ftp) (http)
TXT
Processed data included within Sample table