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Research Articles

Distinguishing Right from Left Colon by the Pattern of Gene Expression

Oleg K. Glebov, Luz M. Rodriguez, Kenneth Nakahara, Jean Jenkins, Janet Cliatt, Casey-Jo Humbyrd, John DeNobile, Peter Soballe, Richard Simon, George Wright, Patrick Lynch, Sherri Patterson, Henry Lynch, Steven Gallinger, Aby Buchbinder, Gary Gordon, Ernest Hawk and Ilan R. Kirsch
Oleg K. Glebov
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Luz M. Rodriguez
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Kenneth Nakahara
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Jean Jenkins
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Janet Cliatt
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Casey-Jo Humbyrd
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John DeNobile
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Peter Soballe
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Richard Simon
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George Wright
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Patrick Lynch
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Sherri Patterson
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Henry Lynch
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Steven Gallinger
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Aby Buchbinder
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Gary Gordon
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Ernest Hawk
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Ilan R. Kirsch
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DOI:  Published August 2003
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  • Fig. 1.
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    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.

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    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.

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    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

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  • Table 1

    Genes that show more than three-fold differences in expression in ascending versus descending adult colon

    GeneCloneUniGene clusterFold-difference L:ATat value
    homeo box D13 IncytePD:3462557Hs.1583098.155.932
    solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2 IncytePD:1634540Hs.1023075.716.656
    serine protease inhibitor, Kazal type, 5 IncytePD:776793Hs.3315555.396.606
    ESTs IncytePD:1671596Hs.1094385.2317.146
    secretory leukocyte protease inhibitor (antileukoproteinase) IncytePD:2510171Hs.2517544.5215.136
    homeo box B13 IncytePD:1861743Hs.667314.317.999
    BRCA1 associated protein IncytePD:1623214Hs.1227644.069.395
    connective tissue growth factor IncytePD:1674454Hs.755114.038.561
    EGF-containing fibulin-like extracellular matrix protein 1 IncytePD:1798209Hs.762244.0311.436
    protease inhibitor 3, skin-derived (SKALP) IncytePD:2503913Hs.1123413.937.209
    NADPH oxidase 1 IncytePD:2793437Hs.1323703.886.904
    solute carrier family 28 (sodium-coupled nucleoside transporter), member 2 IncytePD:1632811Hs.1936653.734.161
    retinoic acid receptor responder (tazarotene induced) 2 IncytePD:1988108Hs.376823.7211.839
    sialyltransferase 1 (β-galactoside α-2,6-sialyltransferase) IncytePD:3211926Hs.3745283.666.651
    osteoblast specific factor 2 (fasciclin I-like) IncytePD:1994715Hs.1363483.514.614
    cysteine-rich protein 1 (intestinal) IncytePD:2121863Hs.31923.411.104
    S100 calcium binding protein P IncytePD:2060823Hs.29623.395.728
    CMP-NeuAC:(β)-N-acetylgalactosaminide (alpha)2,6-sialyltransferase member VIIncytePD:2504517Hs.1096723.3210.432
    family with sequence similarity 3, member C IncytePD:1926135Hs.298823.3212.324
    cysteine-rich, angiogenic inducer, 61 IncytePD:1514989Hs.88673.285.845
    phospholipase A2, group IIA (platelets, synovial fluid) IncytePD:699410Hs.764223.276.014
    protein phosphatase 1, regulatory (inhibitor) subunit 12B IncytePD:1998571Hs.1307603.1818.759
    somatostatin IncytePD:2494617Hs.124093.114.037
    chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) IncytePD:1669647Hs.2373563.0811.331
    alpha-actinin-2-associated LIM proteinIncytePD:1924344Hs.1352813.0514.464
    ribonuclease, RNase A family, 1 (pancreatic) IncytePD:3086929Hs.782243.019.321
    3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial) IncytePD:1807407Hs.598890.33−8.154
    acyl-Coenzyme A oxidase 1, palmitoyl IncytePD:1798585Hs.3799910.33−13.088
    carnitine deficiency-associated gene expressed in ventricle 1 IncytePD:1494531Hs.3331200.33−3.798
    glucosaminyl (N-acetyl) transferase 2, I-branching enzyme IncytePD:1966455Hs.9340.32−7.262
    MAWD binding protein IncytePD:1812030Hs.163410.32−4.875
    glypican 3 IncytePD:645584Hs.1196510.32−6.347
    ATP-binding cassette, sub-family G (WHITE), member 2 IncytePD:1501080Hs.1947200.32−8.077
    solute carrier family 38, member 4 IncytePD:778212Hs.1656550.3−6.679
    homeo box B6 IncytePD:606814Hs.984280.3−6.918
    solute carrier family 16 (monocarboxylic acid transporters), member 1 IncytePD:1981569Hs.752310.29−13.71
    differentially expressed in hematopoietic lineages IncytePD:1903267Hs.2733210.28−5.393
    solute carrier family 16 (monocarboxylic acid transporters), member 1 IncytePD:733668Hs.752310.26−12.558
    hydroxy-δ-5-steroid dehydrogenase, 3 β- and steroid δ-isomerase 1 IncytePD:182802Hs.385860.24−6.071
    apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 IncytePD:1634063Hs.5600.24−5.824
    cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18 IncytePD:25957280.22−7.491
    solute carrier family 20 (phosphate transporter), member 1 IncytePD:1846463Hs.784520.2−16.061
    hydroxy-δ-5-steroid dehydrogenase, 3 β- and steroid δ-isomerase 2 IncytePD:942100Hs.8250.2−5.632
    nuclear receptor subfamily 1, group H, member 4 IncytePD:214180Hs.1716830.16−9.444
    alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150) IncytePD:2771046Hs.12390.15−7.824
    paired-like homeodomain transcription factor 2 IncytePD:2794019Hs.922820.13−8.926
    regenerating islet-derived 1 α (pancreatic stone protein, pancreatic thread protein) IncytePD:2923150Hs.10320.11−8.678
    meprin A, βIncytePD:2234609Hs.1947770.08−15.037
    ethanolamine kinase IncytePD:2718565Hs.1204390.07−19.742
    • a L:AT, ratio of descending colon to ascending colon.

  • Table 2

    Genes expressed differentially in ascending and descending colon control all main cellular functions

    CGAPa functional group of genesNo. of genes presented on 9k-arrayNo. of genes expressed differentially in colonb
    TotalOverexpressed in ascending colonOverexpressed in descending colon
    Cell proliferation2343910 (9.1×)29 (3.3×)
    Cell cycle282597 (1.5×)52 (2.5×)
    Cell death1382311 (1.9×)12 (3.1×)
    Cell-cell signalling134135 (1.5×)8 (3.1×)
    Cell adhesion122213 (1.8×)18 (3.1×)
    Embryogenesis and morphogenesis6651 (3.1×)4 (3.3×)
    Developmental processes126277 (3.1×)20 (8.1×)
    Signal transduction5037424 (6.2×)50 (3.2×)
    Angiogenesis93141 (6.7×)13 (3.1×)
    DNA replication, damage, and adducts166333 (6.7×)30 (3.1×)
    Response to external stimulus4967519 (2.9×)56 (5.4×)
    Stress response285386 (2.9×)32 (5.4×)
    Oncogenes177368 (2.6×)28 (3.3×)
    Tumor suppressor genes101236 (1.8×)17 (3.3×)
    Transcription factors2173110 (6.2×)21 (3.0×)
    Receptors, ligands, and receptor signalling proteins172227 (6.7×)15 (3.1×)
    EGF signalling21303 (1.8×)
    TGFβ signalling10000
    Wnt signalling1852 (1.6×)3 (1.6×)
    Insulin signalling16303 (1.8×)
    Ras signalling1642 (1.4×)2 (1.8×)
    Integrin signalling2341 (1.3×)3 (1.8×)
    EGF, TGFβ, Wnt, insulin, Ras, and integrin signalling (one set, no repeating genes)76155 (1.6×)10 (1.8×)
    • a CGAP, Cancer Genome Anatomy Project.

    • b At 0.001 level; maximal fold difference shown in parentheses.

Additional Files

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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.
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Cancer Epidemiology Biomarkers & Prevention: 12 (8)
August 2003
Volume 12, Issue 8
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Distinguishing Right from Left Colon by the Pattern of Gene Expression
Oleg K. Glebov, Luz M. Rodriguez, Kenneth Nakahara, Jean Jenkins, Janet Cliatt, Casey-Jo Humbyrd, John DeNobile, Peter Soballe, Richard Simon, George Wright, Patrick Lynch, Sherri Patterson, Henry Lynch, Steven Gallinger, Aby Buchbinder, Gary Gordon, Ernest Hawk and Ilan R. Kirsch
Cancer Epidemiol Biomarkers Prev August 1 2003 (12) (8) 755-762;

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Distinguishing Right from Left Colon by the Pattern of Gene Expression
Oleg K. Glebov, Luz M. Rodriguez, Kenneth Nakahara, Jean Jenkins, Janet Cliatt, Casey-Jo Humbyrd, John DeNobile, Peter Soballe, Richard Simon, George Wright, Patrick Lynch, Sherri Patterson, Henry Lynch, Steven Gallinger, Aby Buchbinder, Gary Gordon, Ernest Hawk and Ilan R. Kirsch
Cancer Epidemiol Biomarkers Prev August 1 2003 (12) (8) 755-762;
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