Identification of tumor markers in models of human colorectal cancer using a 19,200 element cDNA microarray

Priti Hegde1,3, Rong Qi1, Renee Gaspard1, Kristie Abernathy1, Sonia Dharap1, Julie Earle-Hughes1, Cheryl Gay1, Nnenna U. Nwokekeh1, Alexander I. Saeed1, Vasily Sharov1, Norman H. Lee1, Timothy J. Yeatman2,4, and John Quackenbush1,4

1The Institute for Genomic Research, Rockville, MD, USA

2H. Lee Moffitt Cancer Center, Tampa, FL, USA

3Present address: GlaxoSmithKline, King of Prussia, PA

4Address correspondence to yeatman@moffitt.usf.edu or johnq@tigr.org


Representative differential expression in highly metastatic cell lines, defined by a two-fold or greater change relative to expression in a less metastatic reference, for various functional classes of genes. Ratios and fold induction/repression in red and green represent genes that were overexpressed and underexpressed, respectively, in the highly metastatic cells;  (-) represents genes that could not be called as statistically differentially expressed with high confidence. Each experiment was performed three times. Results are reported for genes with two or more high quality data points.

  L4aSMSWL4aSMSW
Gene_nameTHC_#Expression RatioFold Induction
cell cycle and tumorigenesis 
 
 
 
 
 
 
calpastatinTHC530309
3.45
4.30
2.24
3.45
4.30
2.24
Ki-67 antigenTHC558792
3.26
3.41
-
3.26
3.41
-
cyclinTHC527078
2.20
2.06
-
2.20
2.06
-
G0/G1 switch regulatory phosphoprotein GOS8THC485927
0.13
0.07
-
-7.69
-14.29
-
cell cycle, G1 phase defectTHC483910
0.17
0.12
-
-5.88
-8.33
-
cdc16THC509159
0.42
0.50
-
-2.38
-2.00
-
apoptosis regulator bcl-xTHC512751
2.86
7.03
2.50
2.86
7.03
2.50
Nck-associated protein 1 (Nap1)THC512992
2.42
6.14
3.92
2.42
6.14
3.92
mitotic checkpoint kinase Bub1THC489479
0.44
0.28
0.38
-2.27
-3.57
-2.63
mitotic checkpoint protein kinase BUB1B THC489479
0.16
0.15
0.37
-6.25
-6.67
-2.70
sphingomyelinaseTHC512598
0.45
0.37
-
-2.22
-2.70
-
14-3-3THC512636
2.27
3.5
3.1
2.27
3.50
3.10
NmiTHC556245
2.48
5.26
-
2.48
5.26
-
transcription factors 
 
 
 
 
 
 
transcription factor BTF3bTHC512531
2.59
2.44
0.41
2.59
2.44
-2.44
transcription factor CTF-1, CAAT-bindingTHC506787
0.32
0.27
-
-3.13
-3.70
-
transcription factor ETR101THC554684
2.97
3.31
-
2.97
3.31
-
transcription factor ITF-1THC509691
0.22
0.19
-
-4.55
-5.26
-
transcription factor MADS/MEF2THC563169
0.46
0.44
0.33
-2.17
-2.27
-3.03
transcription factor NFAT5 isoform bTHC480740
0.41
0.31
-
-2.44
-3.23
-
transcription factor NF-kappa-B, p65 subunitTHC529952
0.13
0.14
-
-7.69
-7.14
-
transcription factor S-IITHC493180
2.7
2.76
-
2.70
2.76
-
transcription factor Sp1THC527282
0.14
0.22
-
-7.14
-4.55
-
transcription factor USF2THC558601
0.10
0.09
-
-10.00
-11.11
-
translation elongation factor 1, alphaTHC480091
2.20
2.48
2.05
2.20
2.48
2.05
translation elongation factor 1, betaTHC529810
0.48
0.33
-
-2.08
-3.03
-
translation elongation factor 1, gammaTHC485540
2.17
3.48
6.85
2.17
3.48
6.85
translation initiation factor 2 associated p67THC483408
0.08
0.05
-
-12.50
-20.00
-
Translation initiation factor 2ATHC481279
0.26
0.34
3.24
-3.85
-2.94
3.24
translation initiation factor 4ATHC492573
3.83
5.66
-
3.83
5.66
-
translation initiation factor 4AIITHC481077
4.00
4.31
2.27
4.00
4.31
2.27
translation initiation factor 4BTHC556378
6.12
9.08
2.28
6.12
9.08
2.28
translation initiation factor 5THC547535
0.38
0.27
4.74
-2.63
-3.70
4.74
proto-oncogenes 
 
 
 
 
 
 
proto-oncogene c-K-rasTHC481807
2.43
3.73
-
2.43
3.73
-
proto-oncogene dekTHC506250
2.47
2.52
-
2.47
2.52
-
proto-oncogene ets-2THC559139
1.69
2.84
2.35
1.69
2.84
2.35
proto-oncogene junD THC543521
2.35
3.67
-
2.35
3.67
-
proto-oncogene N-rasTHC512835
2.05
2.64
4.21
2.05
2.64
4.21
proto-oncogene rhoA,THC502870
3.07
5.32
2.28
3.07
5.32
2.28
proto-oncogene bcl-3THC506333
2.84
2.92
-
2.84
2.92
-
oncogenes 
 
 
 
 
 
 
oncogene E6-AP, papillomavirusTHC482127
3.80
3.40
-
3.80
3.40
-
oncogene ret/PTC3THC536717
3.60
5.09
-
3.60
5.09
-
oncogene setTHC526421
3.06
4.02
1.98
3.06
4.02
1.98
Yamaguchi Sarcoma viral oncogene homolog 1 THC483974
2.90
2.70
3.73
2.90
2.70
3.73
growth factors 
 
 
 
 
 
 
Insulin-like growth factor ITHC482770
3.50
3.94
-
3.50
3.94
-
transforming growth factor beta (GB:M60315)THC529873
2.48
6.20
-
2.48
6.20
-
transforming growth factor beta-binding protein, latentTHC506202
0.22
0.22
2.31
-4.55
-4.55
2.31
bone-derived growth factorTHC486169
0.25
0.16
4.55
-4.00
-6.25
4.55
fibroblast growth factor receptor THC553705
0.18
0.34
-
-5.56
-2.94
-
insulin-like growth factor binding protein 1THC529746
-
-
0.15
-
-
-6.67
epidermal growth factor receptorTHC484646
2.17
2.21
-
2.17
2.21
-
Transforming growth factor, alphaTHC498311
2.46
-
4.92
2.46
-
4.92
glycolysis 
 
 
 
 
 
 
Enolase, alphaTHC479319
4.67
11.94
2.45
4.67
11.94
2.45
Pyruvate kinase, M1/M2 typeTHC479467
2.55
3.93
2.89
2.55
3.93
2.89
lactate dehydrogenase BTHC479476
3.10
4.20
-
3.10
4.20
-
glyceraldehyde -3-phosphate dehydrogenaseTHC480123
3.15
4.20
2.03
3.15
4.20
2.03
glucosyltransferaseTHC492734
-
3.92
-
-
3.92
-
GlcNac-1-P transferaseTHC503927
1.70
3.84
-
1.70
3.84
-
glycogen phosphorylase, isoform 3THC479658
2.77
3.72
-
2.77
3.72
-
phosphoenolpyruvate carboxykinaseTHC547596
2.08
3.34
-
2.08
3.34
-
phosphofructokinase, plateletTHC556562
2.14
3.08
-
2.14
3.08
-
glycogen phosphorylase, isoform 2THC493599
-
2.95
-
-
2.95
-
triosephosphate isomeraseTHC492605
2.27
2.79
-
2.27
2.79
-
glycogen phosphorylase, liverTHC547566
2.16
2.70
-
2.16
2.70
-
2,3-bisphosphoglycerate mutaseTHC485574
0.17
0.10
-
-5.88
-10.00
-
phosphoglycerate mutase 2, muscleTHC523404
0.17
0.19
-
-5.88
-5.26
-
aryl hydrocarbon receptor nuclear translocatorTHC553991
3.47
4.39
-
3.47
4.39
-
Aldolase ATHC506082
2.15
2.31
0.26
2.15
2.31
-3.85
cell-matrix proteins 
 
 
 
 
 
 
EpicanTHC482446
-
5.82
4.87
-
5.82
4.87
CofilinTHC484922
4.18
6.53
-
4.18
6.53
-
Profilin ITHC485330
2.92
5.74
-
2.92
5.74
-
Profilin IITHC482718
 
 
3.84
-
-
3.84
collagen, type XI, alpha 2THC504818
3.21
3.15
-
3.21
3.15
-
collagen, Type IX, alpha 1THC530893
-
-
0.33
-
-
-3.03
VinculinTHC530068
2.71
2.99
-
2.71
2.99
-
tubulin, beta d1THC480951
4.90
6.36
2.53
4.90
6.36
2.53
actin, betaTHC563165
10.31
16.05
3.12
10.31
16.05
3.12
actin-capping protein alpha subunit isoform 1THC481578
4.60
9.11
3.78
4.60
9.11
3.78
Catenin, alpha 2(E) 
3.03
2.44
2.92
3.03
2.44
2.92
ATP-dependent metalloprotease YME1LTHC484479
-
-
3.92
-
-
3.92
Annexin IVTHC496004
-
0.57
0.25
-
-1.75
-4.00
Caveolin, 22kDaTHC495762
0.13
0.08
0.30
-7.69
-12.50
-3.33
dynein, light chain 1, cytoplasmicTHC523389
0.49
0.48
0.33
-2.04
-2.08
-3.03
signal transduction 
 
 
 
 
 
 
Guanine nucleotide-binding protein G(s), alpha subunitTHC506149
3.33
7.89
3.61
3.33
7.89
3.61
Guanine nucleotide-binding protein ral, ras relatedTHC493091
-
4.33
2.15
-
4.33
2.15
serine/threonine kinaseTHC519506
2.92
3.22
 
2.92
3.22
-
protein phosphatase 2A, alpha catalytic subunitTHC543416
2.44
3.11
2.24
2.44
3.11
2.24
guanylyl cyclase large subunit, solubleTHC531332
2.38
2.79
-
2.38
2.79
-
Tyrosine kinase THC544138
 
3.62
5.95
-
3.62
5.95
ERK3THC485382
2.54
3.16
-
2.54
3.16
-
Tyrosine phosphatase PAC-1THC484984
0.08
0.04
-
-12.50
-25.00
-
cytosolic phospholipase A2 gamma THC503323
0.14
0.11
-
-7.14
-9.09
-
cytosolic phospholipase A2 beta; cPLA2betaTHC512549
0.46
0.35
-
-2.17
-2.86
-
markers 
 
 
 
 
 
 
mutL homolog hPMS2THC484568
0.10
0.07
-
-10.00
-14.29
-
mutL homolog hPMS1THC502746
0.40
0.26
-
-2.50
-3.85
-
hepatic carcinomas 
 
 
 
 
 
 
phosphatidylethanolamine N-methyltransferaseTHC523125
0.22
0.21
-
-4.55
-4.76
-
hepatoma-derived growth factorTHC502980
2.73
2.76
-
2.73
2.76
-
oncogene tpr/met, translocatedTHC559059
0.13
0.12
-
-7.69
-8.33
-
Hepatocellular carcinoma associated proteinTHC481590
9.43
50.38
6.49
9.43
50.38
6.49