Article Figures & Data
Figures
- Fig. 1.
Hierarchical clustering of genes that are expressed differentially in ascending and descending colon of HNPCC patients. CCP genes (744) were clustered by using average linkage and Pearson correlation coefficient as a distance metric. AT, ascending-colon biopsies; L, descending-colon biopsies. Relative expression: green, overexpression; red, underexpression; black, equal expression; gray, missing value.
- Fig. 2.
Multidimensional scaling of ascending- and descending-colon biopsies from HNPCC and non-HNPCC patients. Axes, relative distance (the magnitude of the projection of the 1-Pearson correlation coefficient distance in each of the first three principal components). Sixty-eight ascending (filled oval) and descending (open oval) colon biopsies were clustered according to expression of 1336 genes.
- Fig. 3.
Multidimensional scaling of ascending and descending fetal colon biopsies. Axes, relative distance (the magnitude of the projection of the 1-Pearson correlation coefficient distance in each of the first three principal components). Twenty-six ascending (filled oval) and descending (open oval) fetal colon biopsies were clustered according to expression of 87 CCP genes.
Tables
- Table 1
Genes that show more than three-fold differences in expression in ascending versus descending adult colon
Gene Clone UniGene cluster Fold-difference L:ATa t value homeo box D13 IncytePD:3462557 Hs.158309 8.15 5.932 solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2 IncytePD:1634540 Hs.102307 5.71 6.656 serine protease inhibitor, Kazal type, 5 IncytePD:776793 Hs.331555 5.39 6.606 ESTs IncytePD:1671596 Hs.109438 5.23 17.146 secretory leukocyte protease inhibitor (antileukoproteinase) IncytePD:2510171 Hs.251754 4.52 15.136 homeo box B13 IncytePD:1861743 Hs.66731 4.31 7.999 BRCA1 associated protein IncytePD:1623214 Hs.122764 4.06 9.395 connective tissue growth factor IncytePD:1674454 Hs.75511 4.03 8.561 EGF-containing fibulin-like extracellular matrix protein 1 IncytePD:1798209 Hs.76224 4.03 11.436 protease inhibitor 3, skin-derived (SKALP) IncytePD:2503913 Hs.112341 3.93 7.209 NADPH oxidase 1 IncytePD:2793437 Hs.132370 3.88 6.904 solute carrier family 28 (sodium-coupled nucleoside transporter), member 2 IncytePD:1632811 Hs.193665 3.73 4.161 retinoic acid receptor responder (tazarotene induced) 2 IncytePD:1988108 Hs.37682 3.72 11.839 sialyltransferase 1 (β-galactoside α-2,6-sialyltransferase) IncytePD:3211926 Hs.374528 3.66 6.651 osteoblast specific factor 2 (fasciclin I-like) IncytePD:1994715 Hs.136348 3.51 4.614 cysteine-rich protein 1 (intestinal) IncytePD:2121863 Hs.3192 3.4 11.104 S100 calcium binding protein P IncytePD:2060823 Hs.2962 3.39 5.728 CMP-NeuAC:(β)-N-acetylgalactosaminide (alpha)2,6-sialyltransferase member VI IncytePD:2504517 Hs.109672 3.32 10.432 family with sequence similarity 3, member C IncytePD:1926135 Hs.29882 3.32 12.324 cysteine-rich, angiogenic inducer, 61 IncytePD:1514989 Hs.8867 3.28 5.845 phospholipase A2, group IIA (platelets, synovial fluid) IncytePD:699410 Hs.76422 3.27 6.014 protein phosphatase 1, regulatory (inhibitor) subunit 12B IncytePD:1998571 Hs.130760 3.18 18.759 somatostatin IncytePD:2494617 Hs.12409 3.11 4.037 chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) IncytePD:1669647 Hs.237356 3.08 11.331 alpha-actinin-2-associated LIM protein IncytePD:1924344 Hs.135281 3.05 14.464 ribonuclease, RNase A family, 1 (pancreatic) IncytePD:3086929 Hs.78224 3.01 9.321 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial) IncytePD:1807407 Hs.59889 0.33 −8.154 acyl-Coenzyme A oxidase 1, palmitoyl IncytePD:1798585 Hs.379991 0.33 −13.088 carnitine deficiency-associated gene expressed in ventricle 1 IncytePD:1494531 Hs.333120 0.33 −3.798 glucosaminyl (N-acetyl) transferase 2, I-branching enzyme IncytePD:1966455 Hs.934 0.32 −7.262 MAWD binding protein IncytePD:1812030 Hs.16341 0.32 −4.875 glypican 3 IncytePD:645584 Hs.119651 0.32 −6.347 ATP-binding cassette, sub-family G (WHITE), member 2 IncytePD:1501080 Hs.194720 0.32 −8.077 solute carrier family 38, member 4 IncytePD:778212 Hs.165655 0.3 −6.679 homeo box B6 IncytePD:606814 Hs.98428 0.3 −6.918 solute carrier family 16 (monocarboxylic acid transporters), member 1 IncytePD:1981569 Hs.75231 0.29 −13.71 differentially expressed in hematopoietic lineages IncytePD:1903267 Hs.273321 0.28 −5.393 solute carrier family 16 (monocarboxylic acid transporters), member 1 IncytePD:733668 Hs.75231 0.26 −12.558 hydroxy-δ-5-steroid dehydrogenase, 3 β- and steroid δ-isomerase 1 IncytePD:182802 Hs.38586 0.24 −6.071 apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 IncytePD:1634063 Hs.560 0.24 −5.824 cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18 IncytePD:2595728 0.22 −7.491 solute carrier family 20 (phosphate transporter), member 1 IncytePD:1846463 Hs.78452 0.2 −16.061 hydroxy-δ-5-steroid dehydrogenase, 3 β- and steroid δ-isomerase 2 IncytePD:942100 Hs.825 0.2 −5.632 nuclear receptor subfamily 1, group H, member 4 IncytePD:214180 Hs.171683 0.16 −9.444 alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150) IncytePD:2771046 Hs.1239 0.15 −7.824 paired-like homeodomain transcription factor 2 IncytePD:2794019 Hs.92282 0.13 −8.926 regenerating islet-derived 1 α (pancreatic stone protein, pancreatic thread protein) IncytePD:2923150 Hs.1032 0.11 −8.678 meprin A, β IncytePD:2234609 Hs.194777 0.08 −15.037 ethanolamine kinase IncytePD:2718565 Hs.120439 0.07 −19.742 -
a L:AT, ratio of descending colon to ascending colon.
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- Table 2
Genes expressed differentially in ascending and descending colon control all main cellular functions
CGAPa functional group of genes No. of genes presented on 9k-array No. of genes expressed differentially in colonb Total Overexpressed in ascending colon Overexpressed in descending colon Cell proliferation 234 39 10 (9.1×) 29 (3.3×) Cell cycle 282 59 7 (1.5×) 52 (2.5×) Cell death 138 23 11 (1.9×) 12 (3.1×) Cell-cell signalling 134 13 5 (1.5×) 8 (3.1×) Cell adhesion 122 21 3 (1.8×) 18 (3.1×) Embryogenesis and morphogenesis 66 5 1 (3.1×) 4 (3.3×) Developmental processes 126 27 7 (3.1×) 20 (8.1×) Signal transduction 503 74 24 (6.2×) 50 (3.2×) Angiogenesis 93 14 1 (6.7×) 13 (3.1×) DNA replication, damage, and adducts 166 33 3 (6.7×) 30 (3.1×) Response to external stimulus 496 75 19 (2.9×) 56 (5.4×) Stress response 285 38 6 (2.9×) 32 (5.4×) Oncogenes 177 36 8 (2.6×) 28 (3.3×) Tumor suppressor genes 101 23 6 (1.8×) 17 (3.3×) Transcription factors 217 31 10 (6.2×) 21 (3.0×) Receptors, ligands, and receptor signalling proteins 172 22 7 (6.7×) 15 (3.1×) EGF signalling 21 3 0 3 (1.8×) TGFβ signalling 10 0 0 0 Wnt signalling 18 5 2 (1.6×) 3 (1.6×) Insulin signalling 16 3 0 3 (1.8×) Ras signalling 16 4 2 (1.4×) 2 (1.8×) Integrin signalling 23 4 1 (1.3×) 3 (1.8×) EGF, TGFβ, Wnt, insulin, Ras, and integrin signalling (one set, no repeating genes) 76 15 5 (1.6×) 10 (1.8×) -
a CGAP, Cancer Genome Anatomy Project.
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b At 0.001 level; maximal fold difference shown in parentheses.
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. Supplementary Data: Glebov et al., CEBP Volume 12: 755-762, 2003
Supplementary Figures and Tables
Files in this Data Supplement:
- Supplementary Figure 1 - Fig. 1. Hierarchical clustering of genes that are expressed differentially in ascending and descending colon of non-HNPCC patients. 658 CCP genes were clustered using average linkage and Pearson correlation coefficient as distance metric. AT, AT-biopsies; L, L-biopsies. Relative expression: green, overexpression; red, underexpression; black, equal expression; gray, missing value.
- Supplementary Figure 2 - Fig. 2. Hierarchical clustering of genes that are expressed differentially in ascending and descending colon of HNPCC and non-HNPCC patients. 1336 CCP genes were clustered using average linkage and Pearson correlation coefficient as distance metric. AT, AT-biopsies; L, L-biopsies. Relative expression: green, overexpression; red, underexpression; black, equal expression; gray, missing value.
- Supplementary Figure 3 - Fig. 3. Hierarchical clustering of genes that are expressed differentially in ascending and descending colon of HNPCC and non-HNPCC patients without surgery. 1349 CCP genes were clustered using average linkage and Pearson correlation coefficient as distance metric. AT, AT-biopsies; L, L-biopsies. Relative expression: green, overexpression; red, underexpression; black, equal expression; gray, missing value.
- Supplementary Figure 4 - Fig. 4. Hierarchical clustering of genes that are expressed differentially in ascending and descending fetal colon. 87 CCP genes were clustered using average linkage and Pearson correlation coefficient as distance metric. AT, AT-biopsies; L, L-biopsies. Relative expression: green, overexpression; red, underexpression; black, equal expression; gray, missing value.
- Supplementary Table 1 - Table 1. 744 CCP genes expressed differentially in ascending versus descending colon of HNPCC patients.
- Supplementary Table 2 - Table 2. 658 CCP genes expressed differentially in ascending versus descending colon of non-HNPCC patients.
- Supplementary Table 3 - Table 3. 1336 CCP genes expressed differentially in ascending versus descending colon of HNPCC and non-HNPCC patients.
- Supplementary Table 4 - Table 4. 1349 CCP genes expressed differentially in ascending versus descending colon of HNPCC and non-HNPCC patients without surgery.
- Supplementary Table 5 - Table 5. 87 CCP genes expressed differentially in ascending versus descending fetal colon.
August 2003
Volume 12, Issue 8
Volume 12, Issue 8
Distinguishing Right from Left Colon by the Pattern of Gene Expression
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