exprLoi2008: Gene expression data used in the DEGraph package vignette
In DEGraph: Two-sample tests on a graph
Description
Usage
Format
Details
Author(s)
Source
References
Examples
Description
This data set gives gene expression data for a subset of 227
genes used in the DEGraph package vignette. This comes from the 15737
gene, 255 patient dataset of Loi et al. (2008) which was used to study
resistance to tamoxifen treatment in hormone-dependent breast cancer.
Usage
1
Format
A matrix of 227 lines and 255 columns.
Details
The original data set corresponds to data processed by RMA and median-centered
as available from the GSE6532 GEO archive:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6532.
These data were summarized from the probe set level to the gene level as
follows. The expression level of a gene was defined as the expression level
of the probe set with largest alignment score among all probe sets mapping
to this gene according to the annotation in GSE6532. When the largest
alignment score was achieved by several probe sets, the median expression
level of those probe sets was taken.
Author(s)
Laurent Jacob, Pierre Neuvial and Sandrine Dudoit
Source
Loi et al.,
Predicting prognosis using molecular profiling in estrogen
receptor-positive breast cancer treated with tamoxifen.
BMC Genomics, 9(1):239, 2008.
References
Loi et al.,
Predicting prognosis using molecular profiling in estrogen
receptor-positive breast cancer treated with tamoxifen.
BMC Genomics, 9(1):239, 2008.
Examples
1
2
3
4
data("Loi2008_DEGraphVignette")
dim(exprLoi2008)
head(exprLoi2008)
Example output
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.21.0 (2016-10-30) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, gc, load, save
R.utils v2.5.0 (2016-11-07) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, inherits, isOpen, parse, warnings
[1] 227 255
OXFT_1070 OXFT_1089 OXFT_1097 OXFT_1103 OXFT_1107 OXFT_1120
31 0.63154724 1.1013662 0.07666683 1.15192391 0.21149008 0.39701695
32 2.39392605 -0.2990676 1.63097058 -0.08162808 -0.44328808 0.00542666
207 -0.43491920 -0.2014332 -0.17474313 -0.79355904 0.51156061 0.39712217
208 -0.12407434 -0.1436049 -0.19797114 0.16743783 0.01208414 -0.03814792
355 -0.04402282 0.2880910 0.82617199 -0.27103061 -0.29948738 -0.42582058
356 0.07432790 0.0000000 -0.08551320 0.12975925 -0.11671890 -0.10324929
OXFT_1125 OXFT_1127 OXFT_1133 OXFT_1142 OXFT_114 OXFT_1156
31 -0.03121462 -0.42248424 0.96200907 -0.49085921 0.1273771964 -0.20998605
32 -0.02886077 -0.67550123 -0.21762824 -0.10701428 -0.8447943134 -0.14571754
207 0.42705962 1.07432017 0.75346833 -0.11173981 0.0007315712 1.03790432
208 -0.06715869 0.13710951 -0.01646298 -0.05440749 -0.0776500804 0.01600699
355 -0.00959760 -0.22533225 -0.32113770 0.85234159 -0.3702710153 0.14458670
356 -0.02175809 0.02666275 0.13977262 -0.08997312 -0.1552699478 -0.02734948
OXFT_1157 OXFT_1167 OXFT_1168 OXFT_116 OXFT_1173 OXFT_1177
31 -0.25377248 0.550250771 -0.1604880 0.244748323 0.32830804 -1.15891413
32 0.98697765 0.121075086 2.1799809 1.218666090 -0.79076668 -0.48351669
207 -0.21259563 0.289691925 -0.3319112 -0.138483100 -0.69714897 0.04792422
208 0.02103061 0.006207989 0.1790327 0.003314849 0.09216802 -0.13017197
355 -0.36942515 -0.378666724 0.6546544 -0.292693807 0.51389949 1.05301708
356 -0.05390844 0.064280594 0.1144459 0.056666022 -0.03782070 0.42279948
OXFT_1181 OXFT_1193 OXFT_1200 OXFT_124 OXFT_1301 OXFT_1320
31 -0.09126411 -0.87857431 1.065117647 -0.21716518 -0.30212773 -0.07315612
32 0.92847689 0.02846398 1.187366393 0.01346485 -0.02810010 0.38302113
207 0.18744971 0.00000000 0.900704273 0.24955643 -0.03372971 0.52890476
208 -0.09689554 0.16019658 -0.008457742 0.10982547 0.21104486 -0.23978951
355 0.19734677 -0.23736098 -0.385451483 -0.06239326 -0.19631126 0.07571284
356 -0.02700799 0.10545526 -0.093520810 -0.04279225 0.02986184 -0.02207525
OXFT_1331 OXFT_1397 OXFT_1432 OXFT_1441 OXFT_1525 OXFT_1579
31 0.371210721 -0.138766506 0.30818098 0.66768566 0.66527349 -0.180363964
32 -0.844100073 0.345885650 -0.46113558 -0.81314800 -0.04650723 1.526320963
207 0.412139659 -0.477547904 0.43291685 0.49460038 -0.76832240 0.293985322
208 0.001952023 0.037844536 0.08633959 0.37222504 -0.07224956 -0.042713223
355 0.873974417 0.125967637 -0.05782936 0.04513288 -0.14733262 0.152896094
356 -0.026773773 -0.005171895 0.02506654 -0.04807684 0.02601665 -0.007379958
OXFT_1766 OXFT_1769 OXFT_1770 OXFT_1800 OXFT_1804 OXFT_1818
31 0.00883009 -0.18936371 -0.4653008 0.62823691 -0.230608976 1.276648525
32 0.70505109 0.20751695 -0.9597477 -0.02568145 -0.533881814 -0.630778433
207 -0.29408877 -0.52965738 -0.4953984 -0.25517889 -0.732951267 0.093082193
208 -0.16220647 -0.03506686 0.3187851 -0.23632243 0.107882860 -0.007048503
355 0.38636591 -0.08967020 -0.3900409 0.26929318 -0.006010086 -0.300307853
356 0.03429446 -0.04406437 -0.1322038 -0.06183940 -0.005787794 -0.115319754
OXFT_1821 OXFT_1889 OXFT_1902 OXFT_192 OXFT_1939 OXFT_1962
31 0.02017503 0.55976127 -0.01023596 -0.47262173 -0.07643601 0.4619223
32 -0.68436105 0.45677229 -0.19077548 -0.63586884 -0.68306021 -1.0046140
207 0.09915569 0.37072478 0.05565125 -0.28297867 0.43915156 0.4080101
208 -0.23228186 0.05768533 0.04143514 -0.14480814 -0.21493179 -0.2093836
355 -0.01370904 -0.34408892 -0.32021043 -0.45693882 0.17333538 0.9663348
356 0.01021373 0.01503111 -0.03215910 -0.03686483 -0.30551923 0.3764038
OXFT_1981 OXFT_1982 OXFT_2002 OXFT_2005 OXFT_2027 OXFT_2057
31 -0.068758142 -0.48926551 0.9382999 0.24168715 -0.55724271 0.667999244
32 0.268965015 0.32322384 0.1101265 0.41184341 1.05512095 -0.320386381
207 -0.002771938 -0.38821156 -0.5049154 0.51674714 0.64765350 0.199242705
208 -0.049480176 -0.24099958 -0.1863979 -0.11598992 -0.05328892 0.047878598
355 -0.423974670 0.29164231 0.2223469 0.69083237 0.37053299 0.015905290
356 -0.059564161 -0.09701679 -0.0803410 -0.04060105 0.07087440 -0.004869227
OXFT_2069 OXFT_209 OXFT_2175 OXFT_2190 OXFT_2220 OXFT_2338
31 0.926451588 -0.04513291 0.08339060 0.95904493 -0.56697646 -1.431462182
32 0.008700407 -0.37609022 -0.15900258 -1.03339730 -0.06672361 -0.165475731
207 0.171544777 0.43744731 0.07636007 0.06972740 -0.35804987 -0.293701410
208 0.003402176 -0.07860051 -0.03841571 -0.03047027 0.05396851 -0.008357235
355 0.017279900 -0.27204911 0.11742803 -0.27462442 0.31062570 1.736105444
356 -0.087373784 -0.03278219 0.06568413 0.06812729 0.23707742 0.483172063
OXFT_2340 OXFT_2341 OXFT_3597 OXFT_375 OXFT_380 OXFT_412
31 0.68540830 0.43374120 -0.32095429 0.05083879 -0.25293119 1.205988798
32 0.28069076 -0.82242060 0.17460891 0.08532444 0.30812967 0.184323397
207 0.05721942 0.94289622 1.16329362 0.62596287 -0.06382699 0.144476215
208 0.07556075 0.17970692 -0.08758154 0.14746681 0.15938991 -0.004646772
355 0.18689723 -0.10094706 0.19736402 -0.20858779 -0.14583637 -0.367022936
356 -0.06618010 -0.03524458 0.04425944 0.21211868 0.28234774 0.122626766
OXFT_427 OXFT_429 OXFT_443 OXFT_4904 OXFT_511 OXFT_5210
31 -0.868099749 -0.52231819 -0.52720070 0.21180380 -0.15440168 -0.84423642
32 0.003960758 0.25435072 -0.08371677 -0.49787760 1.39261056 -0.56253275
207 -0.030734687 -0.34625930 -0.86147657 -0.13776417 0.11458942 -0.03177599
208 0.378059696 -0.20765448 0.20546425 0.21570129 0.13353628 -0.14449000
355 0.112046195 -0.09054167 -0.22524855 -0.36134280 -0.03668621 0.31913731
356 0.181368510 -0.09744090 0.06365924 -0.05860906 0.24003532 -0.03975546
OXFT_550 OXFT_555 OXFT_55 OXFT_588 OXFT_595 OXFT_596
31 0.6184467 -0.4991562 0.24837159 -0.25702330 -0.44642629 0.1642149
32 0.3283202 -0.2246136 -0.19770461 0.03297452 0.85800564 0.8813473
207 -0.3061940 -0.4487316 0.57272228 -0.36475703 -0.36562445 -0.7442016
208 0.3496525 0.1570964 -0.04004254 0.03885414 0.04037673 0.3765488
355 -0.3165164 0.5430285 -0.22488323 -0.05473762 0.41126604 -0.3701626
356 0.0195094 0.1200365 -0.03024157 0.08475764 -0.03309309 0.2403760
OXFT_619 OXFT_638 OXFT_669 OXFT_676 OXFT_680 OXFT_697
31 0.18596400 0.16718585 0.00000000 0.5687745 0.03141271 -0.32432715
32 -0.22022775 0.75142754 -0.47713332 -0.7099872 -0.04385982 0.24609368
207 0.68618272 -0.08060355 -0.35738365 1.2610264 0.08460773 -0.21451160
208 0.39846427 0.08269300 0.07831466 -0.1223899 -0.04755363 0.02923602
355 -0.45234212 -0.28586761 -0.39345199 0.1476776 -0.19977320 0.05364916
356 0.09791399 0.01481813 0.07091111 0.2930464 0.13439553 0.25569795
OXFT_700 OXFT_705 OXFT_706 OXFT_711 OXFT_729 OXFT_736
31 0.20213094 -0.4482803 -0.793737194 0.48578537 -0.8641960 -1.0687365
32 0.59164359 -0.3207912 0.001277955 0.07340339 -0.4278133 0.9873897
207 0.53417594 -0.5285459 0.197264617 0.08403474 0.2705274 0.1305624
208 -0.08422812 0.2012864 -0.314008125 0.26946365 0.1018483 0.2436850
355 0.19865071 0.4003276 0.165831721 -0.48116861 0.5774677 -0.3694118
356 -0.02192413 0.1588277 -0.236332820 0.11502375 0.1347110 0.1937313
OXFT_738 OXFT_742 OXFT_771 OXFT_779 OXFT_829 OXFT_837
31 0.42920950 -0.18052437 -0.3645432614 -0.892499700 0.69660567 0.17586093
32 0.03287605 0.78607930 1.0099015580 -0.616313306 0.57381073 -0.29713763
207 0.08227472 -0.19560974 -0.1403145666 -0.047304863 -0.54283721 0.08939634
208 0.11264189 0.25631094 0.0009033664 -0.102683432 0.02268302 -0.07892879
355 0.01511513 -0.34857971 0.1923681941 -0.007476335 -0.08426265 -0.01952199
356 -0.01227913 0.04323717 0.3206870478 0.140233107 0.04368779 -0.06173409
OXFT_848 OXFT_849 OXFT_876 OXFT_887 OXFT_890 OXFT_894
31 -0.12887479 -0.671894574 0.26367249 0.39372580 -0.048923116 0.39384870
32 0.07343494 1.585670349 -0.16709459 -0.09706122 -0.120139208 0.05733324
207 -0.49777064 -0.788713831 -0.02169237 -0.27832138 1.159725400 0.02742887
208 -0.04680294 -0.016017214 0.03574453 0.14647163 -0.143742820 0.10006821
355 -0.08538760 0.425306445 0.50936186 0.31814169 -0.040845704 -0.04383099
356 -0.16227450 -0.004141094 0.03747579 0.05036295 -0.003346166 -0.02577854
OXFT_913 OXFT_928 OXFT_944 KIT_104B91 KIT_112B55 KIT_114B68
31 0.06857754 -0.03794627 -1.45934863 0.04227732 0.07554960 0.43071769
32 1.72613271 0.33976212 0.47944125 -0.59191462 0.34494353 -0.12970792
207 -0.24535873 -0.39790638 -0.81793295 -0.06923619 0.16208187 0.22153864
208 -0.12980731 -0.21071004 -0.11185825 -0.25124874 -0.14955033 -0.06274501
355 0.38032023 0.39045301 0.01216701 0.38417432 -0.06468088 -0.31826903
356 -0.07827197 0.02010315 -0.05783635 0.02907270 -0.00228192 0.30567455
KIT_130B92 KIT_131B79 KIT_135B40 KIT_138B34 KIT_148B49 KIT_14B98
31 0.04860204 -0.09267746 0.15481551 -0.16692417 -0.01744031 0.23887508
32 -0.35269915 0.05686858 0.36508090 1.05908888 0.01088198 0.03434699
207 0.00000000 0.18890786 0.02389817 -0.04176494 0.01552684 -0.34765395
208 0.42342535 0.44046125 -0.03375360 -0.02239729 0.06333007 0.15493034
355 -0.69387013 0.15882531 0.36898535 -0.46297692 0.22901619 0.48643357
356 0.08381717 -0.14615176 0.03372659 0.08358488 0.02171980 -0.19935643
KIT_150B81 KIT_154B42 KIT_159B47 KIT_15C94 KIT_162B98 KIT_165B72
31 0.0000000 -0.4206975 0.14567108 -0.38181084 0.2482703 0.14790298
32 0.3785445 -0.7887862 -0.60593194 0.29073099 -0.2794820 -0.08540355
207 0.2134819 0.0000000 1.22315039 -0.69912321 0.1625025 -0.52150814
208 0.1876546 0.1310837 -0.01559244 0.03321861 0.1276523 -0.32049724
355 -0.2901596 -0.5623498 0.17200467 0.20159906 -0.3487370 0.47950261
356 0.1008833 -0.1979099 0.08248057 0.30685746 0.4696793 0.36723049
KIT_166B79 KIT_169B79 KIT_170B15 KIT_171B77 KIT_173B43 KIT_17C40
31 0.577810985 -0.6299828 -0.47125563 0.62853567 -0.2210944 -0.26296795
32 -0.060793893 0.7202689 -0.18537289 -0.47952150 0.9841421 1.47588276
207 -0.088386924 0.1304933 -0.24010888 0.08623644 -0.2194192 0.23472247
208 0.002434564 -0.4117986 0.64716627 -0.22996603 -0.2584932 -0.05983319
355 -0.624465508 1.0641490 -0.50152328 -0.40351379 0.1874221 -0.14612213
356 -0.165616861 -0.1271881 -0.02005356 0.00000000 -0.1636151 -0.11920745
KIT_183B75 KIT_191B79 KIT_194B60 KIT_202B44 KIT_203B49 KIT_207C08
31 0.09257134 -0.45531202 0.29711861 -0.002713434 0.21643479 0.7821961
32 -0.17566943 0.73065937 -0.71804192 0.239250484 0.60930388 0.4705619
207 -0.47102522 0.85918868 0.25752311 -0.298523545 -0.52348961 1.0725760
208 -0.08260284 0.29221912 -0.17877154 -0.276952773 -0.25050044 -0.4421469
355 0.03458413 0.04161822 -0.30311251 1.276714400 0.47201163 0.5867475
356 -0.33095812 -0.14183607 0.08815067 -0.040061525 0.09060527 -0.1084371
KIT_212C21 KIT_216C61 KIT_225C52 KIT_230C47 KIT_235C20 KIT_238C87
31 -0.4351408 -0.43799783 -0.21301125 0.6746289 -0.064062895 0.045102756
32 -0.1599444 -0.23043334 -0.36243890 -0.6232767 -0.409069813 0.013893066
207 -0.6025640 -0.43878648 0.05114430 0.2586043 0.155201596 -0.002078385
208 0.4600938 0.36060452 -0.23766878 0.1210734 0.110387122 -0.108988069
355 0.9387972 0.68629180 -0.15518852 -0.2723572 0.119931547 0.146886959
356 0.3061699 -0.03685951 -0.02927526 -0.2809306 -0.007809571 -0.158666049
KIT_239C32 KIT_244C89 KIT_252C64 KIT_254C80 KIT_256C45 KIT_271C71
31 0.3722879 -0.33591134 -0.250779621 -0.35730377 -0.1927514 1.7470353
32 1.1687170 -0.30513393 -0.319464636 0.62880140 -0.6912420 -0.4237211
207 -0.3080457 0.02628776 -0.373801544 0.04392672 0.1648503 0.2704830
208 -0.2218937 -0.01640968 -0.267669813 0.14993213 -0.2672903 0.2692731
355 0.6643786 -0.41294103 0.008458011 -0.40389956 0.2815494 0.0248308
356 -0.2510710 -0.22857080 0.140212014 0.26501926 -0.1979099 0.0683291
KIT_27C82 KIT_288C57 KIT_289C75 KIT_291C17 KIT_298C47 KIT_301C66
31 -0.166663035 -0.26900409 -0.74919658 -0.46414886 0.1174921 0.8900627
32 -0.252159241 0.75979504 0.34376384 -0.56559066 0.4377054 0.5457807
207 -0.597921697 -0.22836792 -0.23548970 0.06567791 -0.3261175 -0.1052859
208 0.427459228 0.18709334 0.15169801 -0.17693711 0.3364669 0.2598149
355 1.503320344 -0.31424785 0.01332736 0.18329429 -0.3140478 0.0957737
356 0.003009586 0.05107258 0.09486335 0.11544985 0.1840736 0.0799609
KIT_307C50 KIT_311A27 KIT_313A87 KIT_35C29 KIT_39C24 KIT_40C57
31 0.788540046 -0.6380506 -0.70170808 -0.03844443 0.3607228 0.95706332
32 -0.502034174 0.2667566 -0.57545198 -0.08530109 -0.1023567 1.33237237
207 -0.001831992 0.1854038 0.32020312 -0.36581875 -0.3174674 0.15328463
208 0.394620700 0.2311241 0.03405725 -0.31719335 -0.4261914 0.18793343
355 -0.614260978 -0.7018015 -0.20284256 0.90976971 0.8921406 0.32230458
356 -0.222049066 -0.1191484 0.45136475 -0.04398259 -0.1277170 0.08469673
KIT_41C65 KIT_48A46 KIT_51A98 KIT_53A06 KIT_55A79 KIT_56A94
31 0.4926069 0.1971257 -0.42483384 -0.03196542 0.6671129 -0.14533283
32 -0.0427435 0.8896506 -0.34141619 0.25429074 0.8421052 1.63231555
207 -0.2397697 -0.2727763 -0.02793098 -0.24460686 0.7400349 -0.03475068
208 -0.1583308 0.2062451 0.02559615 -0.05522145 0.1779155 0.12399477
355 0.5912453 0.4012649 -0.12224422 -0.17176554 -0.4685912 -0.14060516
356 -0.1001161 -0.1215541 0.29527111 -0.16361514 0.4357806 0.09152918
KIT_64A59 KIT_67A43 KIT_69A93 KIT_6B85 KIT_72A92 KIT_77A50
31 -0.24246223 1.51298153 -0.06162322 0.25041494 -0.6430350 -0.251704481
32 -0.37803197 -0.55526516 -0.10022940 0.09921256 1.0292881 1.482385407
207 0.36985119 0.15941464 0.16419847 0.76322560 -0.4264738 -0.008119519
208 -0.04700448 -0.07999136 -0.14133386 0.04331126 0.1247672 0.088450301
355 0.14003222 -0.24564164 0.34352496 -0.47860042 0.3267799 0.309597486
356 0.30580926 -0.02461891 0.04141259 -0.13118187 0.2191645 -0.007231671
KIT_7B96 KIT_82A83 KIT_84A44 KIT_85A03 KIT_8B87 KIT_96A21
31 0.15495785 1.0468281 0.2597093 -0.19181580 -0.344693811 -0.61359401
32 0.15688005 -0.0856385 0.2072503 0.48940147 0.514373419 0.44430588
207 0.27652102 0.7858248 -0.1929817 0.56209970 0.861043316 0.45553047
208 -0.08302138 0.3470298 0.3607859 0.30740448 -0.008399242 0.05839447
355 -0.27501714 -0.6447979 -0.2595368 -0.78902322 -0.011754202 -0.25371003
356 -0.04429680 -0.2195220 -0.1401184 -0.05366419 0.220771401 0.25307508
GUYT_50102 GUYT_50105 GUYT_50106 GUYT_50107 GUYT_50108 GUYT_50109
31 -0.84989949 0.04390644 0.58641628 0.606176287 -0.18753162 -0.58221695
32 -0.30624057 -0.05200336 -0.06017899 0.004189536 -0.30032353 -0.46874515
207 0.76769141 0.18557121 0.12740521 0.178169990 0.03498844 0.12872765
208 -0.09845469 -0.15810979 0.04682626 -0.112096252 -0.11290243 0.03923577
355 -0.02212564 -0.87503574 0.55376967 1.034839249 0.07419876 0.15001675
356 0.00000000 -0.16285663 -0.03274827 0.248873642 -0.02445781 -0.11263092
GUYT_50110 GUYT_50111 GUYT_50112 GUYT_50115 GUYT_50116 GUYT_50117
31 0.74121915 -1.5668385 0.87342347 -0.67900539 0.04581151 -0.75254859
32 -0.07099521 -0.1362879 0.94191600 0.56732327 1.00397834 0.74661611
207 -0.12331429 0.1270504 -0.19417667 0.88168610 0.07920501 -0.40298970
208 -0.33482736 -0.1541433 -0.04715937 -0.11727536 0.06199693 -0.11783005
355 1.16709737 -0.1728388 0.36268894 -0.60199598 0.13407992 1.88968595
356 -0.07991048 0.2984376 0.22792927 0.04783381 0.01687475 0.08269269
GUYT_50118 GUYT_50119 GUYT_50120 GUYT_50122 GUYT_50124 GUYT_50125
31 0.11974173 0.31239482 -0.31262916 -0.05931332 1.529652914 0.36395297
32 -0.23654300 -0.19837442 0.18943604 -1.39754616 0.009471822 0.31902204
207 0.48525946 -0.50470785 0.68485357 0.94862177 0.536023410 0.39965657
208 -0.06044877 0.08069597 -0.03552932 -0.01023620 -0.105563578 -0.01982631
355 -0.41035238 1.22382337 0.73338914 0.90753577 0.141961975 1.58970193
356 -0.01647885 0.02687376 0.74825964 0.59378347 0.428749527 0.04255127
GUYT_50126 GUYT_50128 GUYT_50130 GUYT_50131 GUYT_50132 GUYT_50134
31 0.4248085 -0.15981495 -0.1643816 -0.263047038 -0.20177702 1.09600406
32 0.1786262 0.45862294 -0.5496220 0.593920282 0.43842675 -0.89404641
207 0.4717008 0.09918438 -0.7716738 0.006018916 0.47702405 1.12122815
208 0.1485889 -0.07061638 0.1387766 0.311858938 -0.32505986 0.03629985
355 -0.2365361 0.96379222 0.3010414 0.274621826 0.09426795 0.50067849
356 1.0155725 -0.15241941 -0.1530573 0.078650212 0.45543649 0.08200287
GUYT_50135 GUYT_50136 GUYT_50137 GUYT_50138 GUYT_50143 GUYT_50146
31 -0.31136225 1.02132622 0.40269853 0.24304710 -0.5109186122 -0.09456852
32 -1.06034026 0.95537062 1.48172823 -0.06808322 -0.3267327774 1.62507173
207 0.45653210 -0.39215647 -0.03226917 -0.03408297 -0.7547460028 0.36925609
208 -0.12324165 -0.05595707 0.06857250 -0.09134518 0.0002761202 -0.11696043
355 1.02846340 -1.52753651 -0.97146388 -0.67177011 1.1373184161 -0.37465753
356 -0.09537212 -0.25247757 0.05993202 -0.07232274 0.8539774961 0.24709300
GUYT_50148 GUYT_50149 GUYT_50150 GUYT_50151 GUYT_50153 GUYT_50154
31 -0.56627644 0.349624959 0.32860717 -0.88514425 -0.18278222 -0.34183319
32 -0.08839581 -0.055491291 0.75860454 1.17150230 -0.70644931 -0.97044767
207 0.55480559 0.006653706 0.44568969 -0.09305810 0.15078579 0.26438428
208 0.08421193 0.030870050 0.34427374 0.05584519 0.26316969 0.21500577
355 0.48414158 0.999355203 -0.09044665 0.73040349 -0.64429821 -0.02831968
356 0.34858551 0.189018615 0.03223858 0.14740935 -0.08975853 0.15533491
GUYT_50155 GUYT_50156 GUYT_50158 GUYT_50159 GUYT_50160 GUYT_50162
31 -1.3686434 0.30970733 -1.31276495 0.46928835 0.216157317 1.33000610
32 -0.8951112 -0.15204592 -0.14448134 -0.81045594 -0.537512570 -0.08366280
207 0.9579482 0.01040384 -0.72369995 -0.46478265 0.087062552 1.07211243
208 0.1397461 0.21999496 0.02998063 -0.01702882 -0.008184381 -0.08078662
355 1.1785954 -0.61581483 1.05474261 1.26738781 0.935367990 1.19508573
356 0.5113253 -0.09468328 0.77755244 0.22231541 -0.203768656 -0.32431595
GUYT_50163 GUYT_50166 GUYT_50168 GUYT_50169 GUYT_50172 GUYT_50173
31 0.03684611 -0.6346079 -0.01272166 -0.43707615 -0.2763339 -0.779773535
32 0.52833985 -0.4033055 1.17739843 1.10577153 -0.1724654 -0.382857007
207 0.33066511 -0.1523634 -0.01700376 -0.30610033 0.4393101 0.000000000
208 0.02108014 -0.1698271 -0.16427281 -0.03774789 -0.0307110 -0.024926650
355 0.37494085 1.0835867 -0.12667746 0.29428684 -0.9841137 0.003136984
356 0.02505086 0.8889358 -0.23330527 -0.08747254 0.1257169 -0.065508871
GUYT_50174 GUYT_50176 GUYT_50177 GUYT_50178 GUYT_50179 GUYT_50181
31 0.14225654 -0.05789950 -0.71653058 0.46591662 0.3507601 -0.20005172
32 0.81616944 -0.59432103 -0.54702330 0.30979024 1.9786962 1.45502958
207 -0.06881587 -0.03934176 -0.20924405 -0.96665996 0.3704400 0.09409111
208 -0.02513253 -0.18378616 0.01331116 0.14167746 0.1916589 -0.14438121
355 -0.31177745 -1.10629704 0.53297863 -0.59169365 -0.1946492 0.00389833
356 -0.28172596 -0.29413837 0.37652055 -0.08183422 -0.0478295 0.33139078
GUYT_50182 GUYT_50183 GUYT_50184 GUYT_50188 GUYT_50190 GUYT_50192
31 -0.53200595 2.130659e-02 0.62867208 0.05463333 -0.02844567 0.51972232
32 0.18066645 3.653520e-01 -1.10049255 -0.18721128 1.10101606 -0.12612606
207 -0.14113308 -2.556045e-05 0.50633621 0.45882185 -0.83334349 -0.35743302
208 -0.05942983 -2.157284e-01 0.08444636 -0.32485308 -0.08753506 -0.30796586
355 0.02094779 -1.612069e-01 -0.11176078 -0.98190479 -1.80768096 -0.67165150
356 -0.23478421 -3.165361e-01 -0.20820383 -0.01920127 -0.15392164 -0.01033121
GUYT_50193 GUYT_50200 GUYT_50204 GUYT_50210 GUYT_50211 GUYT_50213
31 0.132991631 0.4752113 0.328841282 0.92463089 -0.68130800 -0.27875037
32 1.032643235 1.2986672 -0.359485289 0.37962503 -0.28628739 0.21659011
207 -0.311556039 -0.1700616 0.452396800 -0.97948092 -0.21523280 -0.43790912
208 0.002448055 0.1965165 -0.094158799 0.02902521 -0.09212114 0.07265608
355 -0.858118160 -1.8336562 -0.660555296 -0.15586687 -0.71932135 0.41713568
356 -0.256008633 -0.2035257 -0.007846447 -0.07217577 -0.25487514 0.67574046
GUYT_50218 GUYT_50219 GUYT_50221 GUYT_50223 GUYT_50225 GUYT_50228
31 0.324929073 0.8952180 0.9514528 0.09565457 0.4455968 0.02497276
32 0.407770142 -0.4085945 -0.5858376 1.40438488 -0.4023060 0.89262177
207 -0.218007234 -0.2026194 0.1605310 -0.27668606 -0.6938556 -0.88666635
208 0.038396535 0.3222863 0.0791160 -0.12279797 -0.2736178 0.04684644
355 0.387647827 -1.7652368 -0.1382927 -1.53334705 0.1116891 0.35373301
356 -0.007392446 -0.4156084 0.1698907 -0.13875818 0.1339423 0.38064826
GUYT_50230 GUYT_50233 GUYT_50235 GUYT_50236 GUYT_50237 GUYT_50238
31 0.0000000 0.94022759 -0.67712739 0.61147492 -0.19965972 -0.71797826
32 1.0112878 -0.05619529 0.38197662 -0.49572999 -0.28620430 1.26006371
207 0.1056913 0.14129120 -0.17708033 -0.05295347 -1.10129433 1.14442874
208 0.5416695 -0.26418366 -0.19334329 0.24812151 0.11321728 -0.05991895
355 0.1267939 -0.65286540 0.46357950 -1.28263532 -0.80525989 -1.24415255
356 0.1092597 0.45118125 -0.05852099 0.09910943 -0.04449359 -0.30561840
GUYT_50239 GUYT_50243 GUYT_50246 GUYT_50247 GUYT_50248 GUYT_50251
31 -0.32623746 -0.07032121 -0.37657979 0.016171644 -0.3211107 -0.9455222
32 0.05281503 1.24471419 -0.05706395 -1.184929343 -1.3400636 0.1875034
207 -0.62648826 -0.33551641 0.07012959 -0.615504980 -0.5359786 -0.2478521
208 0.42760719 0.09230377 0.07034493 -0.019246215 0.1519448 0.3383353
355 -0.19005750 -0.68217564 -0.34684009 0.923604147 0.3636000 -1.9213821
356 0.08405862 -0.11186656 -0.08095464 0.007686603 0.6946456 0.2439483
GUYT_50252 GUYT_50254 GUYT_50257
31 0.47315289 -0.33225829 -0.33169935
32 -1.02445434 0.42593822 -0.68427326
207 -0.44312918 -0.43060689 0.41511758
208 0.29352947 -0.18071684 -0.27187932
355 -0.11191037 0.01594593 0.22791100
356 0.03266993 -0.01459625 -0.06449261
DEGraph documentation built on Nov. 8, 2020, 5:52 p.m.
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Description Usage Format Details Author(s) Source References Examples
Description
This data set gives gene expression data for a subset of 227 genes used in the DEGraph package vignette. This comes from the 15737 gene, 255 patient dataset of Loi et al. (2008) which was used to study resistance to tamoxifen treatment in hormone-dependent breast cancer.
Usage
1 |
Format
A matrix of 227 lines and 255 columns.
Details
The original data set corresponds to data processed by RMA and median-centered as available from the GSE6532 GEO archive: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6532.
These data were summarized from the probe set level to the gene level as follows. The expression level of a gene was defined as the expression level of the probe set with largest alignment score among all probe sets mapping to this gene according to the annotation in GSE6532. When the largest alignment score was achieved by several probe sets, the median expression level of those probe sets was taken.
Author(s)
Laurent Jacob, Pierre Neuvial and Sandrine Dudoit
Source
Loi et al., Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics, 9(1):239, 2008.
References
Loi et al., Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics, 9(1):239, 2008.
Examples
1 2 3 4 | data("Loi2008_DEGraphVignette")
dim(exprLoi2008)
head(exprLoi2008)
|
Example output
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.21.0 (2016-10-30) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, gc, load, save
R.utils v2.5.0 (2016-11-07) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, inherits, isOpen, parse, warnings
[1] 227 255
OXFT_1070 OXFT_1089 OXFT_1097 OXFT_1103 OXFT_1107 OXFT_1120
31 0.63154724 1.1013662 0.07666683 1.15192391 0.21149008 0.39701695
32 2.39392605 -0.2990676 1.63097058 -0.08162808 -0.44328808 0.00542666
207 -0.43491920 -0.2014332 -0.17474313 -0.79355904 0.51156061 0.39712217
208 -0.12407434 -0.1436049 -0.19797114 0.16743783 0.01208414 -0.03814792
355 -0.04402282 0.2880910 0.82617199 -0.27103061 -0.29948738 -0.42582058
356 0.07432790 0.0000000 -0.08551320 0.12975925 -0.11671890 -0.10324929
OXFT_1125 OXFT_1127 OXFT_1133 OXFT_1142 OXFT_114 OXFT_1156
31 -0.03121462 -0.42248424 0.96200907 -0.49085921 0.1273771964 -0.20998605
32 -0.02886077 -0.67550123 -0.21762824 -0.10701428 -0.8447943134 -0.14571754
207 0.42705962 1.07432017 0.75346833 -0.11173981 0.0007315712 1.03790432
208 -0.06715869 0.13710951 -0.01646298 -0.05440749 -0.0776500804 0.01600699
355 -0.00959760 -0.22533225 -0.32113770 0.85234159 -0.3702710153 0.14458670
356 -0.02175809 0.02666275 0.13977262 -0.08997312 -0.1552699478 -0.02734948
OXFT_1157 OXFT_1167 OXFT_1168 OXFT_116 OXFT_1173 OXFT_1177
31 -0.25377248 0.550250771 -0.1604880 0.244748323 0.32830804 -1.15891413
32 0.98697765 0.121075086 2.1799809 1.218666090 -0.79076668 -0.48351669
207 -0.21259563 0.289691925 -0.3319112 -0.138483100 -0.69714897 0.04792422
208 0.02103061 0.006207989 0.1790327 0.003314849 0.09216802 -0.13017197
355 -0.36942515 -0.378666724 0.6546544 -0.292693807 0.51389949 1.05301708
356 -0.05390844 0.064280594 0.1144459 0.056666022 -0.03782070 0.42279948
OXFT_1181 OXFT_1193 OXFT_1200 OXFT_124 OXFT_1301 OXFT_1320
31 -0.09126411 -0.87857431 1.065117647 -0.21716518 -0.30212773 -0.07315612
32 0.92847689 0.02846398 1.187366393 0.01346485 -0.02810010 0.38302113
207 0.18744971 0.00000000 0.900704273 0.24955643 -0.03372971 0.52890476
208 -0.09689554 0.16019658 -0.008457742 0.10982547 0.21104486 -0.23978951
355 0.19734677 -0.23736098 -0.385451483 -0.06239326 -0.19631126 0.07571284
356 -0.02700799 0.10545526 -0.093520810 -0.04279225 0.02986184 -0.02207525
OXFT_1331 OXFT_1397 OXFT_1432 OXFT_1441 OXFT_1525 OXFT_1579
31 0.371210721 -0.138766506 0.30818098 0.66768566 0.66527349 -0.180363964
32 -0.844100073 0.345885650 -0.46113558 -0.81314800 -0.04650723 1.526320963
207 0.412139659 -0.477547904 0.43291685 0.49460038 -0.76832240 0.293985322
208 0.001952023 0.037844536 0.08633959 0.37222504 -0.07224956 -0.042713223
355 0.873974417 0.125967637 -0.05782936 0.04513288 -0.14733262 0.152896094
356 -0.026773773 -0.005171895 0.02506654 -0.04807684 0.02601665 -0.007379958
OXFT_1766 OXFT_1769 OXFT_1770 OXFT_1800 OXFT_1804 OXFT_1818
31 0.00883009 -0.18936371 -0.4653008 0.62823691 -0.230608976 1.276648525
32 0.70505109 0.20751695 -0.9597477 -0.02568145 -0.533881814 -0.630778433
207 -0.29408877 -0.52965738 -0.4953984 -0.25517889 -0.732951267 0.093082193
208 -0.16220647 -0.03506686 0.3187851 -0.23632243 0.107882860 -0.007048503
355 0.38636591 -0.08967020 -0.3900409 0.26929318 -0.006010086 -0.300307853
356 0.03429446 -0.04406437 -0.1322038 -0.06183940 -0.005787794 -0.115319754
OXFT_1821 OXFT_1889 OXFT_1902 OXFT_192 OXFT_1939 OXFT_1962
31 0.02017503 0.55976127 -0.01023596 -0.47262173 -0.07643601 0.4619223
32 -0.68436105 0.45677229 -0.19077548 -0.63586884 -0.68306021 -1.0046140
207 0.09915569 0.37072478 0.05565125 -0.28297867 0.43915156 0.4080101
208 -0.23228186 0.05768533 0.04143514 -0.14480814 -0.21493179 -0.2093836
355 -0.01370904 -0.34408892 -0.32021043 -0.45693882 0.17333538 0.9663348
356 0.01021373 0.01503111 -0.03215910 -0.03686483 -0.30551923 0.3764038
OXFT_1981 OXFT_1982 OXFT_2002 OXFT_2005 OXFT_2027 OXFT_2057
31 -0.068758142 -0.48926551 0.9382999 0.24168715 -0.55724271 0.667999244
32 0.268965015 0.32322384 0.1101265 0.41184341 1.05512095 -0.320386381
207 -0.002771938 -0.38821156 -0.5049154 0.51674714 0.64765350 0.199242705
208 -0.049480176 -0.24099958 -0.1863979 -0.11598992 -0.05328892 0.047878598
355 -0.423974670 0.29164231 0.2223469 0.69083237 0.37053299 0.015905290
356 -0.059564161 -0.09701679 -0.0803410 -0.04060105 0.07087440 -0.004869227
OXFT_2069 OXFT_209 OXFT_2175 OXFT_2190 OXFT_2220 OXFT_2338
31 0.926451588 -0.04513291 0.08339060 0.95904493 -0.56697646 -1.431462182
32 0.008700407 -0.37609022 -0.15900258 -1.03339730 -0.06672361 -0.165475731
207 0.171544777 0.43744731 0.07636007 0.06972740 -0.35804987 -0.293701410
208 0.003402176 -0.07860051 -0.03841571 -0.03047027 0.05396851 -0.008357235
355 0.017279900 -0.27204911 0.11742803 -0.27462442 0.31062570 1.736105444
356 -0.087373784 -0.03278219 0.06568413 0.06812729 0.23707742 0.483172063
OXFT_2340 OXFT_2341 OXFT_3597 OXFT_375 OXFT_380 OXFT_412
31 0.68540830 0.43374120 -0.32095429 0.05083879 -0.25293119 1.205988798
32 0.28069076 -0.82242060 0.17460891 0.08532444 0.30812967 0.184323397
207 0.05721942 0.94289622 1.16329362 0.62596287 -0.06382699 0.144476215
208 0.07556075 0.17970692 -0.08758154 0.14746681 0.15938991 -0.004646772
355 0.18689723 -0.10094706 0.19736402 -0.20858779 -0.14583637 -0.367022936
356 -0.06618010 -0.03524458 0.04425944 0.21211868 0.28234774 0.122626766
OXFT_427 OXFT_429 OXFT_443 OXFT_4904 OXFT_511 OXFT_5210
31 -0.868099749 -0.52231819 -0.52720070 0.21180380 -0.15440168 -0.84423642
32 0.003960758 0.25435072 -0.08371677 -0.49787760 1.39261056 -0.56253275
207 -0.030734687 -0.34625930 -0.86147657 -0.13776417 0.11458942 -0.03177599
208 0.378059696 -0.20765448 0.20546425 0.21570129 0.13353628 -0.14449000
355 0.112046195 -0.09054167 -0.22524855 -0.36134280 -0.03668621 0.31913731
356 0.181368510 -0.09744090 0.06365924 -0.05860906 0.24003532 -0.03975546
OXFT_550 OXFT_555 OXFT_55 OXFT_588 OXFT_595 OXFT_596
31 0.6184467 -0.4991562 0.24837159 -0.25702330 -0.44642629 0.1642149
32 0.3283202 -0.2246136 -0.19770461 0.03297452 0.85800564 0.8813473
207 -0.3061940 -0.4487316 0.57272228 -0.36475703 -0.36562445 -0.7442016
208 0.3496525 0.1570964 -0.04004254 0.03885414 0.04037673 0.3765488
355 -0.3165164 0.5430285 -0.22488323 -0.05473762 0.41126604 -0.3701626
356 0.0195094 0.1200365 -0.03024157 0.08475764 -0.03309309 0.2403760
OXFT_619 OXFT_638 OXFT_669 OXFT_676 OXFT_680 OXFT_697
31 0.18596400 0.16718585 0.00000000 0.5687745 0.03141271 -0.32432715
32 -0.22022775 0.75142754 -0.47713332 -0.7099872 -0.04385982 0.24609368
207 0.68618272 -0.08060355 -0.35738365 1.2610264 0.08460773 -0.21451160
208 0.39846427 0.08269300 0.07831466 -0.1223899 -0.04755363 0.02923602
355 -0.45234212 -0.28586761 -0.39345199 0.1476776 -0.19977320 0.05364916
356 0.09791399 0.01481813 0.07091111 0.2930464 0.13439553 0.25569795
OXFT_700 OXFT_705 OXFT_706 OXFT_711 OXFT_729 OXFT_736
31 0.20213094 -0.4482803 -0.793737194 0.48578537 -0.8641960 -1.0687365
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OXFT_738 OXFT_742 OXFT_771 OXFT_779 OXFT_829 OXFT_837
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207 0.08227472 -0.19560974 -0.1403145666 -0.047304863 -0.54283721 0.08939634
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OXFT_848 OXFT_849 OXFT_876 OXFT_887 OXFT_890 OXFT_894
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OXFT_913 OXFT_928 OXFT_944 KIT_104B91 KIT_112B55 KIT_114B68
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KIT_130B92 KIT_131B79 KIT_135B40 KIT_138B34 KIT_148B49 KIT_14B98
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KIT_150B81 KIT_154B42 KIT_159B47 KIT_15C94 KIT_162B98 KIT_165B72
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KIT_166B79 KIT_169B79 KIT_170B15 KIT_171B77 KIT_173B43 KIT_17C40
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KIT_183B75 KIT_191B79 KIT_194B60 KIT_202B44 KIT_203B49 KIT_207C08
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KIT_212C21 KIT_216C61 KIT_225C52 KIT_230C47 KIT_235C20 KIT_238C87
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KIT_239C32 KIT_244C89 KIT_252C64 KIT_254C80 KIT_256C45 KIT_271C71
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KIT_27C82 KIT_288C57 KIT_289C75 KIT_291C17 KIT_298C47 KIT_301C66
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KIT_307C50 KIT_311A27 KIT_313A87 KIT_35C29 KIT_39C24 KIT_40C57
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KIT_41C65 KIT_48A46 KIT_51A98 KIT_53A06 KIT_55A79 KIT_56A94
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KIT_64A59 KIT_67A43 KIT_69A93 KIT_6B85 KIT_72A92 KIT_77A50
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KIT_7B96 KIT_82A83 KIT_84A44 KIT_85A03 KIT_8B87 KIT_96A21
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GUYT_50102 GUYT_50105 GUYT_50106 GUYT_50107 GUYT_50108 GUYT_50109
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GUYT_50110 GUYT_50111 GUYT_50112 GUYT_50115 GUYT_50116 GUYT_50117
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GUYT_50118 GUYT_50119 GUYT_50120 GUYT_50122 GUYT_50124 GUYT_50125
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GUYT_50126 GUYT_50128 GUYT_50130 GUYT_50131 GUYT_50132 GUYT_50134
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GUYT_50135 GUYT_50136 GUYT_50137 GUYT_50138 GUYT_50143 GUYT_50146
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GUYT_50148 GUYT_50149 GUYT_50150 GUYT_50151 GUYT_50153 GUYT_50154
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GUYT_50155 GUYT_50156 GUYT_50158 GUYT_50159 GUYT_50160 GUYT_50162
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GUYT_50163 GUYT_50166 GUYT_50168 GUYT_50169 GUYT_50172 GUYT_50173
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GUYT_50174 GUYT_50176 GUYT_50177 GUYT_50178 GUYT_50179 GUYT_50181
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GUYT_50182 GUYT_50183 GUYT_50184 GUYT_50188 GUYT_50190 GUYT_50192
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GUYT_50193 GUYT_50200 GUYT_50204 GUYT_50210 GUYT_50211 GUYT_50213
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GUYT_50218 GUYT_50219 GUYT_50221 GUYT_50223 GUYT_50225 GUYT_50228
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GUYT_50230 GUYT_50233 GUYT_50235 GUYT_50236 GUYT_50237 GUYT_50238
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