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Series GSE6988 Query DataSets for GSE6988
Status Public on Feb 01, 2008
Title Whole genome analysis for liver metastasis gene signitures in colorectal cancer
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Liver metastasis is one of the major causes of death in colorectal cancer (CRC) patients. To understand this process, we investigated whether the gene expression profiling of matched colorectal carcinomas and liver metastases could reveal key molecular events involved in tumor progression and metastasis. We performed experiments using a cDNA microarray containing 17,104 genes with the following tissue samples: paired tissues of 25 normal colorectal mucosa, 27 primary colorectal tumors, 13 normal liver and 27 liver metastasis, and 20 primary colorectal tumors without liver metastasis. To remove the effect of normal cell contamination, we selected 4,583 organ-specific genes with a false discovery rate (FDR) of 0.0067% by comparing normal colon and liver tissues using significant analysis of microarray, and these genes were excluded from further analysis. We then identified and validated 46 liver metastasis-specific genes with an accuracy of 83.3% by comparing the expression of paired primary colorectal tumors and liver metastases using prediction analysis of microarray. The 46 selected genes contained several known oncogenes and 2 ESTs. To confirm that the results correlated with the microarray expression patterns, we performed RT-PCR with WNT5A and carbonic anhydrase II. Additionally, we observed that 21 of the 46 genes were differentially expressed (FDR = 2.27%) in primary tumors with synchronous liver metastasis compared with primary tumors without liver metastasis. We scanned the human genome using a cDNA microarray and identified 46 genes that may play an important role in the progression of liver metastasis in CRC.
Keywords: gene expression profiling using cDNA microarray
 
Overall design We performed 17K cDNA microarray with the amplified RNAs from the following tissue samples: normal colorectal mucosa, primary colorectal tumors, normal liver and liver metastasis tumors, and primary colorectal tumors without liver metastasis. Organ-specific genes in normal colon and liver tissues were excluded from the pre-filtered genes, and then we discovered and validated liver metastasis-specific genes commonly up-regulated in the primary colorectal tumors and liver metastasis tumors. To confirm the microarray data, we performed a RT-PCR of two genes (WNT5A and carbonic anhydrase II) in the primary colorectal tumors with and without liver metastases.
 
Contributor(s) KI D, CHUNG H, PARK C, KANG S, LEE G, KIM N, JEUNG H, RHA S
Citation(s) 17640062
Submission date Feb 08, 2007
Last update date Jan 18, 2013
Contact name DONG HYUK KI
E-mail(s) dki@ic.sunysb.edu
Phone 82-2-2228-8047
Fax 82-2-362-5592
Organization name NBRC
Street address sinchon-dong 134
City Seoul
ZIP/Postal code 120-752
Country South Korea
 
Platforms (1)
GPL4811 Human 17K cDNA-GeneTrack
Samples (123)
GSM160549 Human colorectal liver metastasis tumor (adenocarcinoma) NBRC-AD15889L
GSM160827 Human normal colorectal mucosa NBRC-AD15889N
GSM160828 Human colorectal primary tumor (adenocarcinoma) NBRC-AD15889T2
Relations
BioProject PRJNA99259

Print-tip Lowess normalized data (duplicate spots are averaged) header descriptions
Accession
GSM160827
GSM160835
GSM160966
GSM160969
GSM160973
GSM160977
GSM160982
GSM160981
GSM160987
GSM160991
GSM160995
GSM160998
GSM161003
GSM161002
GSM161013
GSM161016
GSM161019
GSM161022
GSM161026
GSM161030
GSM161033
GSM161037
GSM161041
GSM161050
GSM161056
GSM161060
GSM161009
GSM161008
GSM160830
GSM160828
GSM160837
GSM160967
GSM160970
GSM160974
GSM160978
GSM160984
GSM160983
GSM160988
GSM160992
GSM160996
GSM160999
GSM161005
GSM161004
GSM161014
GSM161017
GSM161020
GSM161023
GSM161028
GSM161027
GSM161031
GSM161034
GSM161038
GSM161042
GSM161053
GSM161051
GSM161057
GSM161062
GSM161011
GSM161010
GSM161046
GSM161044
GSM160549
GSM160834
GSM160965
GSM160968
GSM160972
GSM160976
GSM160980
GSM160986
GSM160990
GSM160994
GSM160997
GSM161001
GSM161000
GSM161012
GSM161015
GSM161018
GSM161021
GSM161025
GSM161029
GSM161032
GSM161036
GSM161040
GSM161049
GSM161007
GSM161006
GSM161055
GSM161059
GSM161048
GSM161045
GSM160832
GSM160971
GSM160975
GSM160979
GSM160985
GSM160989
GSM160993
GSM161024
GSM161035
GSM161039
GSM161043
GSM161054
GSM161058
GSM161063
GSM161064
GSM161065
GSM161066
GSM161067
GSM161070
GSM161071
GSM161072
GSM161073
GSM161074
GSM161075
GSM161076
GSM161077
GSM161078
GSM161079
GSM161080
GSM161081
GSM161082
GSM161083
GSM161084

Data table
Accession GSM160827 GSM160835 GSM160966 GSM160969 GSM160973 GSM160977 GSM160982 GSM160981 GSM160987 GSM160991 GSM160995 GSM160998 GSM161003 GSM161002 GSM161013 GSM161016 GSM161019 GSM161022 GSM161026 GSM161030 GSM161033 GSM161037 GSM161041 GSM161050 GSM161056 GSM161060 GSM161009 GSM161008 GSM160830 GSM160828 GSM160837 GSM160967 GSM160970 GSM160974 GSM160978 GSM160984 GSM160983 GSM160988 GSM160992 GSM160996 GSM160999 GSM161005 GSM161004 GSM161014 GSM161017 GSM161020 GSM161023 GSM161028 GSM161027 GSM161031 GSM161034 GSM161038 GSM161042 GSM161053 GSM161051 GSM161057 GSM161062 GSM161011 GSM161010 GSM161046 GSM161044 GSM160549 GSM160834 GSM160965 GSM160968 GSM160972 GSM160976 GSM160980 GSM160986 GSM160990 GSM160994 GSM160997 GSM161001 GSM161000 GSM161012 GSM161015 GSM161018 GSM161021 GSM161025 GSM161029 GSM161032 GSM161036 GSM161040 GSM161049 GSM161007 GSM161006 GSM161055 GSM161059 GSM161048 GSM161045 GSM160832 GSM160971 GSM160975 GSM160979 GSM160985 GSM160989 GSM160993 GSM161024 GSM161035 GSM161039 GSM161043 GSM161054 GSM161058 GSM161063 GSM161064 GSM161065 GSM161066 GSM161067 GSM161070 GSM161071 GSM161072 GSM161073 GSM161074 GSM161075 GSM161076 GSM161077 GSM161078 GSM161079 GSM161080 GSM161081 GSM161082 GSM161083 GSM161084
ID AD15889N BF95674N BH27060N CA75662N CH76639N DA85401N DA86595N DA86595N2 DB14731N DB33368N DC10136N DC54343N DX46644N DX46644N2 DX63421N DX64153N DX67096N DX70008N DX72875N DX73169N DX73339N DX86797N EX36605N DA09647N DD13676N DX27754N DX57828N DX57828N2 AD15889T AD15889T2 BF95674T BH27060T CA75662T CH76639T DA85401T DA86595T DA86595T2 DB14731T DB33368T DC10136T DC54343T DX46644T DX46644T2 DX63421T DX64153T DX67096T DX70008T DX72875T DX72875T2 DX73169T DX73339T DX86797T EX36605T DA09647T DA09647T2 DD13676T DX27754T DX57828T DX57828T2 EA71820T AX11903T AD15889L BF95674L BH27060L CA75662L CH76639L DA85401L DA86595L DB14731L DB33368L DC10136L DC54343L DX46644L DX46644L2 DX63421L DX64153L DX67096L DX70008L DX72875L DX73169L DX73339L DX86797L EX36605L DA09647L DX57828L DX57828L2 DD13676L DX27754L EA71820L AX11903L AD15889Y CA75662Y CH76639Y DA85401Y DA86595Y DB14731Y DB33368Y DX70008Y DX73339Y DX86797Y EX36605Y DA09647Y DD13676Y DX14048T DX16165T DX18306T DX18618T DX18679T DX22237T DX24121T DX25011T DX26025T DX28973T DX31056T DX31470T DX33570T DX33882T DX33896T DX36208T DX45134T DX52497T DX62184T DX68531T
H13691 -0.07195064 0.22237389 -0.3903508 0.43414068 -0.166318 0.30781204 0.13542648 0.115554966 -1.3594683 -1.5237014 -1.2382548 -0.1489592 0.07537237 0.29549056 -0.17597933 -0.07339374 -0.11004921 -0.49324444 -0.6650805 -0.07282826 -0.62879974 -0.022348614 -1.4870468 -0.78285015 -0.56850415 -0.4625731 -0.67411184 0.4599756 -0.3825679 0.32790595 0.27557126 -0.6516857 -1.2442256 -0.95930356 -0.4817192 -0.12148832 0.08071683 0.5455827 -0.01857141 0.04945107 0.29483038 -0.29982764 -0.43087426 -0.055077426 -0.66544443 0.25567314 -1.7439368 -0.18341048 0.78782225 1.022407 -0.1105359 -0.90227956 -0.42030323 -0.6108991 1.0607812 0.24196842 -0.06940043 0.7423613 0.10264803 -1.443671 -1.5218952 -2.3319197 -0.68400234 -0.024391716 0.38308242 0.01181401 0.019676192 -0.74249655 -0.3713588 -0.708064 -0.243453 -0.53685373 -0.77053803 -0.49525404 0.32329443 0.8189261 1.1554925 -0.7838028 -0.654586 -2.087509 -1.4968851 -1.1640618 -0.7763546 -1.1674529 -0.75994307 -0.8168631 -1.0908705 -1.2968105 -1.2760199 -1.1541284 -1.4026482 -1.0304672 -1.6310034 -1.3458432 -0.7068888 -1.3062996 -0.74964833 -0.49913347 -1.2896775 -0.32041183 -0.8196629 0.92391354 0.34726593 0.014077419 0.93237257 1.3082292 -1.2377304 -2.6124508 -0.65953887
AA045058 -1.466436 -1.5907308 -1.5553036 -0.66086143 -0.79131943 -1.3604668 -0.5549265 -0.593849 -1.4807825 -0.86439496 -0.40263662 -0.86002845 -0.76282865 -0.88823974 -1.0380526 -1.3069782 -0.5620987 -0.6388932 -0.27922487 -0.9997917 -1.7024161 -1.2434716 -2.073676 -0.54952544 -0.23728146 1.5747027 0.12949981 -0.81487024 0.9893976 2.5105479 -1.7867786 -1.9750414
AA676955 -0.1747589 -0.033979595 0.41999048 -0.4865898 0.53157306 -0.3532391 0.26833868 -0.08054576 0.3874127 0.06851932 -0.29277986 -0.10635284 -1.4879202 -1.6227186 -0.76184595 0.024458716 0.4014603 0.3719503 -0.19772421 -0.05468276 -0.02161689 -0.20151581 -0.7628921 0.009443899 -0.82746226 -0.1883064 -1.2025217 -0.9894772 -0.088348426 -0.019029463 0.09368177 -0.59902173 -1.0067325 0.5227642 -0.7723592 0.6747327 0.14610583 0.5282508 -0.30541003 -0.22647381 0.20514819 -1.5046623 -1.2052847 -0.9434613 0.041878056 0.34592402 0.42705178 -0.31782216 -0.15550171 0.045147713 0.07541705 -0.25779706 -0.86230683 -0.3650816 0.4503978 -0.36194462 0.052243445 -1.6875501 -0.60560113 -0.20139559 -0.116115116 -0.18754262 -0.7305446 -0.20997097 -0.78685564 0.53290004 -0.38304317 0.114418365 0.43614936 -0.16844861 -0.06144308 -0.10928029 -1.5914737 -1.6276789 -1.9133306 -0.3166973 0.08633655 0.353276 -0.150629 0.1460151 -0.85032105 -0.22172658 -0.89990056 -0.3599712 -1.0279225 -0.7573564 -1.0115548 0.6227455 -0.23986661 -0.3532504 -0.28595304 -0.88071823 -0.4939054 -0.92708176 -0.5498464 -0.2714622 -0.35476714 -0.8080519 -0.03215719 -0.74905324 -0.6447133 -0.8805381 -1.1465905 -1.3940289 -1.2526299 -0.5474137 -0.93849534 -0.74398863 -1.0287676 -1.4965577 -1.2073975 -1.3142508 -0.38089836 -1.4812745 -1.0528092 -2.179058 0.1903176 -1.3315516 -1.2699525 -0.90018725 -1.0426888 0.2503135 -0.5497789
N53534 -0.49759153 -0.066478446 -0.062523976 -0.16545758 0.17069949 -0.39116552 -0.17708011 -0.38534853 0.19066182 -0.018545318 0.13904649 -0.19557624 -0.4849277 -0.47682467 0.25282925 -0.06779441 -0.039029915 -0.012285126 -0.27746144 0.098381914 0.30018413 -0.3551379 -0.015501977 -0.24727833 -0.019095793 -0.47394052 -0.34945342 -0.03043427 -0.36840835 -0.35036775 -0.27748612 -0.08383527 -0.034200355 -0.2275352 0.082726054 0.047434527 -0.23197886 0.056263257 -0.23505235 -0.10488305 -0.36983222 -0.56859845 -0.3514246 -0.16288868 -0.17276537 -0.15757237 -0.38677612 -0.27459955 -0.26142773 0.013499917 0.18795086 -0.13788243 -0.13658771 -0.41518092 -0.04676023 0.06312676 0.23041148 -0.9853695 -0.4044279 -0.37296087 0.24839503 -0.5480178 -0.11072945 -0.07613999 0.64379984 -0.16273263 0.017608633 -0.075704075 -0.13603278 -0.2468141 0.170535 -0.17047507 0.29535994 0.25045952 1.1500248 -0.1959869 0.5074599 -0.16023497 -0.2033065 0.32928672 -0.2526624 -0.4049767 -0.12323083 0.19280759 0.04433768 0.21357892 0.14414634 0.6932449 -0.03572748 0.23296325 -0.2823386 0.9136194 -0.39050534 -0.24195594 0.039855365 -0.35545433 -0.20196916 -0.41748947 0.35331786 -0.26158497 0.7502473 -0.12037832 0.5804044 -0.3633451 -0.3624277 -0.7205398 0.0701502 -0.26336858 -0.5558881 -0.1222559 0.018883258 -0.6760597 -0.81137323 0.6946885 -0.5849473 0.10135674 0.07361995 -0.47319138 -0.43331742 -0.1734382 -0.40822676 -0.4331181 -0.44369575
AA775616 -2.9634507 -3.8893702 -2.387636 -5.1971517 -2.6549733 -2.7018156 -1.8523672 -3.518061 -1.9105419 -2.08473 -4.2567215 -2.5858312 -2.8268218 -1.9900533 -2.39275 -2.5406816 -2.3360636 -2.433207 -2.3860655 -2.308049 -2.5804365 -4.7542195 -2.2653494 -4.084418 -3.0813773 -3.0728817 -2.338368 -2.4272594 -2.866774 -2.7469082 -2.2230222 -5.115966 -2.801389 -1.9658927 -0.4837148 -1.0551903 -1.0534151 -1.077556 -2.2281063 -2.7298923 -1.7213926 -2.188355 -1.66613 -1.4414436 -1.5061198 0.10476326 -1.9453119 -2.2710686 -1.8462285 -1.1739774 -2.2564785 -4.8149667 -1.8342364 -2.3623984 1.1521742 -0.92493516 -0.6770936 -0.3154785 -3.954865 -1.9323931 -0.54561466 -1.7384301 -0.036922053 -6.066225 -0.86970013 -1.6886455 1.4473838 0.12240738 -0.6730918 -0.7644747 -0.99418557 -0.43239927 -0.33747935 -1.2737703 -2.298618 0.13443609 -0.12729004 -0.80831206 -0.48492074 -2.7509198 -1.9134578 1.167258 -0.8365393 1.2102879 0.9939294 0.8412483 -1.9170675 -0.68093485 -1.140111 -2.330134 -4.853937 -1.8879868 -2.5361092 -1.6328952 -2.1356149 -2.1670382 -2.440084 -1.2415471 -2.1151018 -3.7806392 -2.5256445 -4.7692046 -2.626483 -4.7176375 -2.4291174 -3.8622262 -3.9083223 -2.64431 -4.365022 -3.317039 -6.4284554 -1.0637964 -3.1086738 -0.89068156 -3.146967 -2.3059103 -1.8962988 -2.441255 -3.370274 -1.8564928 -4.05824 -4.2574663
AA703392 0.870593 1.483894 1.6285805 1.6427631 1.9688486 2.046641 1.476128 1.3895347 1.9133061 2.3767974 1.7332134 1.8643997 1.564073 1.2473513 1.3676476 1.5032163 1.8333725 1.7979738 1.9250581 1.8443294 1.5544412 1.6981161 1.4034176 1.3368351 1.1839924 0.79328597 1.1408517 1.3254825 1.2134486 1.0933803 0.46862778 0.7738474 0.31040776 0.43756956 1.3765018 0.84003997 -0.11095722 1.1608534 0.818682 0.6457255 0.9731893 1.1733161 1.3200009 1.5581317 0.91184247 1.1838351 0.65500534 0.2946377 0.08074261 1.5622506 0.2797804 -0.03750945 1.2966545 1.543175 1.6971819 1.865033 0.427563 0.4741929 1.3678888 1.0153302 4.077272 5.5503798 7.149635 7.120655 3.0356681 4.7851167 5.0033197 2.4939265 3.232112 0.5597337 0.90903735 1.5598725 7.564496 3.5505764 5.4856305 4.757199 3.6100202 7.729565 6.471212 4.029154 0.35377112 4.6631002 4.5450306 -0.08993626 2.8009803 5.3635955 4.471987 7.173752 7.3953643 8.033936 7.25958 5.983 6.0845623 9.137102 7.626389 6.375131 6.618903 6.9562144 6.629956 1.4211636 0.6536107 0.1794297 0.70054543 1.4449685 0.6778588 1.1111149 0.049721286 0.44126198 0.22143489 1.2774163 -1.2577703 -0.44862348 0.71670395 1.0800519 1.6843611 0.2846278 0.8614045 -0.88044566
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Total number of rows: 15707

Table truncated, full table size 20483 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary data files not provided
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