Copyright
©2008 The WJG Press and Baishideng.
World J Gastroenterol. Nov 21, 2008; 14(43): 6662-6672
Published online Nov 21, 2008. doi: 10.3748/wjg.14.6662
Published online Nov 21, 2008. doi: 10.3748/wjg.14.6662
Table 1 Clinicopathological features relative to location of sporadic colorectal cancers
Clinicopathologic features | Tumor location1 (No. of patients) | P | ||
R (n = 27) | L (n = 29) | P (n = 28) | ||
Male/Female | 18/9 | 15/14 | 20/8 | 0.273 |
Age | 62 ± 7 | 60 ± 12 | 62 ± 10 | 0.646 |
AJCC stage2, I/II/III/IV | 4/13/6/4 | 4/15/6/4 | 4/10/9/5 | 0.926 |
Tumor differentiation, WD | 22/5 | 29/0 | 24/4 | 0.021 (R vs L) |
+ MD/PD + muc | 0.052 (L vs P) | |||
Synchronous adenoma, -/+ | 18/9 | 23/6 | 14/14 | 0.052 (L vs P) |
LVN invasion, -/+ | 15/12 | 22/7 | 20/8 | 0.236 |
Table 2 Number of differentially expressed genes in terms of molecular changes and clinicopathological features
Parameters | No. of patients (missing) | No. of differentiallyexpressed genes (P < 0.01), total (up/down) |
Molecular changes1, -/+ | ||
APC mutations | 55/27 (2) | 83 (41/42) |
Wnt-activated | 45/38 (1) | 82 (37/45) |
MMR defects | 70/14 | 238 (122/116) |
RAF-mediated | 58/26 | 108 (59/49) |
Altered p53 expression | 24/59 (1) | 125 (57/68) |
Crossover | 64/19 (1) | 92 (44/48) |
Clinicopathologic features | ||
Tumor location2, R/L + P | 27/57 | 1628 (936/692) |
R/L/P | 27/29/28 | 1263 |
AJCC stage3, I + II/III + IV | 50/34 | 195 (103/92) |
Tumor differentiation, WD + MD/PD + muc | 75/9 | 151 (69/82) |
Synchronous adenoma, -/+ | 55/29 | 152 (92/60) |
LVN invasion, -/+ | 57/27 | 279 (147/132) |
Table 3 Differential gene expression associated with molecular changes and clinicopathological features1
Parameters | Symbol | Name | Log2 fold changes | Unadjusted P |
APC mutations | CDH7 | Cadherin 7, type 2 | 0.419885 | 0.00033 |
DYRK1A | DS tyr-(Y)-phosphorylation regulated kinase 1A | 0.326912 | 0.000343 | |
SLC19A2 | Solute carrier family 19 member 2 | -0.48574 | 0.000427 | |
PISD | Phosphatidylserine decarboxylase | 0.272127 | 0.000545 | |
NDUFC1 | NADH dehydrogenase 1, subcomplex unknown | 0.539581 | 0.000572 | |
Wnt-activated alterations | PRAF2 | PRA1 domain family, member 2 | 0.620619 | 0.000205 |
FOXF1 | Forkhead box F1 | -0.93359 | 0.000524 | |
CD99L2 | CD99 molecule-like 2 | 0.753489 | 0.000772 | |
MMR defects | HMGB1 | High-mobility group box 1 | -0.38141 | 3.74E-06 |
MT1X | Metallothionein 1X | 0.965429 | 0.000252 | |
MT1A | Metallothionein 1A | 1.17894 | 0.000351 | |
SUGT1 | SGT1, G2 allele of SKP1 (S. cerevisiae) | -0.34799 | 0.00039 | |
VTI1B | Vesicle transport with t-SNAREs homolog 1B (yeast) | -0.28513 | 0.000435 | |
SST | Somatostatin | 1.24407 | 0.000564 | |
TDG | Thymine-DNA glycosylase | 0.479829 | 0.000946 | |
RAF-mediated alterations | RAB22A | RAB22A, member RAS oncogene family | -0.36017 | 0.000289 |
PPP1R13L | Protein phosphatase 1, regulatory subunit 13 like | 0.823379 | 0.000614 | |
CAST | Calpastatin | 0.285773 | 0.000872 | |
Altered p53 expression | HLA-F | Major histocompatibility complex, class I, F | -0.55645 | 0.000429 |
XRCC3 | XRCC in Chinese hamster cells 3 | -0.26678 | 0.000588 | |
CCDC24 | Coiled-coil domain containing 24 | -0.28995 | 0.000996 | |
Crossover2 | NID2 | Nidogen 2 (osteonidogen) | 0.938223 | 0.000214 |
EGLN3 | egl nine homolog 3 (C. elegans) | 0.740933 | 0.000375 | |
ITIH1 | Inter-alpha (globulin) inhibitor H1 | -0.34777 | 0.0004 | |
CFH | Complement factor H | -0.33826 | 0.000542 | |
ABI3BP | ABI gene family, member 3 binding protein | -0.82558 | 0.000637 | |
NIBP | NIK and IKK binding protein | 0.649949 | 0.000688 | |
SPRR3 | Small praline-rich protein 3 | 0.99738 | 0.000946 | |
AJCC stage3 | PNPT1 | Polyribonucleotide nucleotidyltransferase 1 | 0.716381 | 4.94E-06 |
BAI2 | Brain-specific angiogenesis inhibitor 2 | 0.545369 | 1.57E-05 | |
ADCY1 | Adenylate cyclase 1 (brain) | -0.43437 | 1.97E-05 | |
VEGFC | Vascular endothelial growth factor C | 0.329341 | 9.11E-05 | |
ATAD3B | ATPase family, AAA domain containing 3B | -0.40978 | 0.000108 | |
CAP1 | CAP, adenylate cyclase-associated protein 1 (yeast) | -0.66905 | 0.000405 | |
RPS6KA6 | Ribosomal protein S6 kinase, 90kDa, polypeptide 6 | 0.301665 | 0.000586 | |
FGF5 | Fibroblast growth factor 5 | 0.464162 | 0.000701 | |
LVN invasion | MMP12 | Matrix metallopeptidase 12 (macrophage elastase) | -0.69015 | 7.76E-05 |
RAP1GDS1 | RAP1, GTP-GDP dissociation stimulator 1 | -0.60949 | 9.63E-05 | |
STOML1 | Stomatin (EPB72)-like 1 | -0.39407 | 0.000255 | |
CCL16 | Chemokine (C-C motif) ligand 16 | 0.475838 | 0.000542 | |
NOTCH3 | Notch homolog 3 (Drosophila) | 0.592567 | 0.000679 | |
DHPS | Deoxyhypusine synthase | -0.33131 | 0.000965 | |
Synchronous adenoma | PARP2 | Poly (ADP-ribose) polymerase family, member 2 | 0.573461 | 6.00E-05 |
MRPL21 | Mitochondrial ribosomal protein L21 | 0.243204 | 0.000149 | |
MRPL16 | Mitochondrial ribosomal protein L16 | 0.267004 | 0.000432 | |
MKKS | McKusick-Kaufman syndrome | 0.439584 | 0.000447 | |
LHX2 | LIM homeobox 2 | 0.663108 | 0.000782 |
Table 4 Class prediction accuracies (%) relative to molecular changes and clinicopathological features
Parameters | Genes1 | CCP | DLDA | 1-NN | 3-NN | NC | SVM | BCCP |
Tumor location | 620 | 85 | 86 | 92 | 90 | 86 | 94 | 94 |
Synchronous adenoma | 12 | 58 | 60 | 64 | 63 | 57 | 67 | 65 |
Tumor stage | 22 | 62 | 58 | 58 | 60 | 61 | 54 | 60 |
APC mutations | 12 | 72 | 72 | 57 | 72 | 67 | 73 | 67 |
LVN invasion | 27 | 70 | 69 | 57 | 60 | 68 | 64 | 68 |
MMR defects | 44 | 76 | 77 | 82 | 82 | 76 | 81 | 83 |
p53 alterations | 8 | 65 | 70 | 61 | 73 | 66 | 72 | 79 |
RAF-mediated alterations | 3 | 36 | 35 | 43 | 51 | 36 | 42 | 69 |
Wnt-activated alterations | 9 | 54 | 54 | 61 | 61 | 58 | 49 | 54 |
- Citation: Kim JC, Kim SY, Roh SA, Cho DH, Kim DD, Kim JH, Kim YS. Gene expression profiling: Canonical molecular changes and clinicopathological features in sporadic colorectal cancers. World J Gastroenterol 2008; 14(43): 6662-6672
- URL: https://www.wjgnet.com/1007-9327/full/v14/i43/6662.htm
- DOI: https://dx.doi.org/10.3748/wjg.14.6662