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Table 2 List of the 46 genes evincing a significant change in their mRNA expression both in TGFβ-treated compared to cultures grown in collagen I gel and medium (= TGFβ-treated vs. control) and IMR fibroblast soluble factor-differentiated cultures compared to cultures grown in collagen I gel and medium (= IMR-treated vs. control).

From: Gene expression in TGFbeta-induced epithelial cell differentiation in a three-dimensional intestinal epithelial cell differentiation model

Gene ontology class Gene name GenBank no chromosomal location TGFβ-treated vs. control IMR-treated vs. control ANOVA
     ratio SD p-value FDR ratio SD p-value FDR p-value
A CYP1B1:cytochrome P450, family 1, subfamily B, polypeptide 1 AA448157 2p21 0.66↓ (±0.26) 0.724 0.795 0.68↓ (±0.23) 0.716 1.000 0.669
A UMPS: uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine-5'-decarboxylase) AA426227 3q13 0.65↓ (±0.56) 0.365 0.464 0.68↓ (±0.45) 0.270 1.000 0.173
A GM2A: GM2 ganglioside activator protein AA453978 5q31.3-q33.1 0.36↓ (±0.26) 0.041 0.265 0.45↓ (±0.47) 0.292 1.000 0.279
A AMD1: S-adenosylmethionine decarboxylase 1 R82299 6q21-q22 0.59↓ (±0.28) 0.054 0.265 0.80↓ (±0.50) 0.410 1.000 0.420
A AHCY: S-adenosylhomocysteine hydrolase AA485626 20cen-q13.1 0.65↓ (±0.23) 0.081 0.265 1.30↑ (±0.42) 0.210 1.000 0.347
A HMOX1: heme oxygenase (decycling) 1 T71757 22q12 3.75↑ (±2.58) 0.693 0.769 0.70↓ (±0.54) 0.491 1.000 0.456
A ALAS2: aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia) AA410346 Xp11.21 0.48↓ (±0.15) 0.010 0.225 0.80↓ (±0.41) 0.299 1.000 0.322
C HIST1H2AC: histone 1, H2ac AA453105 6p21.3 0.78↓ (±0.24) 0.369 0.477 0.78↓ (±0.28) 0.180 1.000 0.196
C CDK6: cyclin-dependent kinase 6 H73724 7q21-q22 2.57↑ (±1.34) 0.418 0.525 0.61↓ (±0.34) 0.442 1.000 0.524
C APC7: anaphase-promoting complex subunit 7 T67474 12q13.12 0.77↓ (±0.07) 0.141 0.269 0.80↓ (±0.13) 0.221 1.000 0.211
C LASS4: LAG1 longevity assurance homolog 4 (S. cerevisiae) AA025779 19p13.2 0.62↓ (±0.29) 0.282 0.388 0.73↓ (±0.33) 0.339 1.000 0.268
D RLF: Rearranged L-myc fusion sequence R26070 1p32 0.54↓ (±0.27) 0.467 0.571 0.77↓ (±0.29) 0.540 1.000 0.437
D TCF7: transcription factor 7 (T-cell specific, HMG-box) AA480071 5q31.1 0.76↓ (±0.49) 0.180 0.291 0.80↓ (±0.42) 0.297 1.000 0.258
D TCF8: transcription factor 8 (represses interleukin 2 expression) R22087 10p11.2 0.62↓ (±0.38) 0.371 0.479 0.74↓ (±0.39) 0.392 1.000 0.286
D TCEA2: transcription elongation factor A (SII), 2 AA412500 20q13.33 0.61↓ (±0.36) 0.241 0.345 0.72↓ (±0.33) 0.161 1.000 0.157
E TIE1: tyrosine kinase with immunoglobulin-like and EGF-like domains 1 AA432062 1p34-p33 0.68↓ (±0.20) 0.084 0.265 0.72↓ (±0.13) 0.070 1.000 0.077
E GPA33: glycoprotein A33 (transmembrane) AA055862 1q24.1 0.72↓ (±0.10) 0.679 0.756 0.80↓ (±0.16) 0.752 1.000 0.703
E MAPKAPK2: mitogen-activated protein kinase-activated protein kinase 2 AA455056 1q32 0.61↓ (±0.10) 0.031 0.265 0.80↓ (±0.21) 0.385 1.000 0.488
E PDZD2: PDZ domain containing 2 AA405458 5p13.2 0.62↓ (±0.07) 0.049 0.265 0.83↓ (±0.12) 0.350 1.000 0.428
E PRL:prolactin AA133920 6p22.2-p21.3 0.66↓ (±0.31) 0.368 0.470 0.69↓ (±0.29) 0.375 1.000 0.357
E AKAP12:A kinase (PRKA) anchor protein (gravin) 12 AA478542 6q24-q25 0.75↓ (±0.41) 0.246 0.351 0.77↓ (±0.35) 0.256 1.000 0.287
E STAM: signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 AA485996 10p14-p13 0.56↓ (±0.26) 0.186 0.297 0.82↓ (±0.16) 0.382 1.000 0.396
E CARP: cardiac ankyrin repeat protein, cytokine inducible nuclear protein C193 AA488072 10q23.31 0.77↓ (±0.16) 0.038 0.265 0.82↓ (±0.17) 0.073 1.000 0.080
E MS4A1: membrane-spanning 4-domains, subfamily A, member 1 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide N91385 11q12-q13.1 1.24↑ (±0.66) 0.612 0.699 1.63↑ (±0.62) 0.323 1.000 0.302
E DRPLA: dentatorubral-pallidoluysian atrophy (atrophin-1) H08642 12p13.31 0.65↓ (±0.42) 0.330 0.436 0.80↓ (±0.53) 0.364 1.000 0.256
E PRKCB1: protein kinase C, beta 1/cDNA DKFZp761J0720 AA479102 16p11.2 1.70↑ (±0.75) 0.392 0.499 0.69↓ (±0.19) 0.376 1.000 0.557
E FPR1: formyl peptide receptor 1 AA425249 19q13.4 0.44↓ (±0.25) 0.018 0.261 0.79↓ (±0.37) 0.371 1.000 0.436
E PLCG1: phospholipase C, gamma 1 (formerly subtype 148) R76365 20q12-q13.1 0.48↓ (±0.23) 0.050 0.265 0.81↓ (±0.48) 0.656 1.000 0.646
E ARHGAP8: Rho GTPase activating protein 8 R69153 22q13.31 0.61↓ (±0.09) 0.017 0.261 0.80↓ (±0.23) 0.307 1.000 0.334
F REN: renin AA455535 1q32 0.44↓ (±0.32) 0.133 0.269 0.88↓ (±0.62) 0.385 1.000 0.326
F PSMD2: proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 AA455193 3q27.1 0.72↓ (±0.39) 0.341 0.448 0.73↓ (±0.50) 0.362 1.000 0.280
F SERPINB6: serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6 AA410517 6p25 0.72↓ (±0.13) 0.369 0.477 0.74↓ (±0.27) 0.254 1.000 0.193
F CRYAB: srystallin, alpha B AA504943 11q22.3-q23.1 0.50↓ (±0.08) 0.096 0.265 0.72↓ (±0.30) 0.219 1.000 0.199
F TGM2: transglutaminase 2 (C polypeptide. protein-glutamine-gamma-glutamyltransferase) R97066 20q12 0.62↓ (±0.30) 0.171 0.284 0.73↓ (±0.24) 0.182 1.000 0.151
G C5: somplement component 5 N73030 9q32-q34 0.74↓ (±0.09) 0.175 0.286 0.76↓ (±0.35) 0.206 1.000 0.122
H COL5A1: collagen, type V, alpha 1 R75635 9q35 0.64↓ (±0.04) 0.618 0.704 0.78↓ (±0.28) 0.783 1.000 0.744
H PNUTL2: peanut-like 2 (Drosophila), T64878 17q22-q23 0.81↓ (±0.15) 0.408 0.514 1.15↑ (±0.08) 0.505 1.000 0.520
H COL18A1: collagen, type XVIII, alpha 1 W07798 21q22.3 0.57↓ (±0.17) 0.164 0.279 0.84↓ (±0.22) 0.411 1.000 0.414
I ATP6V0B: ATPase, H+ transporting, lysosomal 21 kD, V0 subunit c" AA480826 1p32.3 0.69↓ (±0.05) 0.213 0.320 0.84↓ (±0.26) 0.244 1.000 0.276
I BZAP45: basic leucine-zipper protein BZAP45 AA463591 2q33 0.46↓ (±0.25) 0.151 0.273 0.73↓ (±0.30) 0.259 1.000 0.226
I ATP6IP1: ATPase, H+ transporting, lysosomal interacting protein 1 AA488715 Xq28 0.44↓ (±0.32) 0.205 0.312 0.84↓ (±0.48) 0.391 1.000 0.315
J EST R00591 4p16.1 3.20↑ (±1.50) 0.445 0.550 0.78↓ (±0.48) 0.455 1.000 0.572
J RIPX: rap2 interacting protein x R74171 4q21.1 0.62↓ (±0.20) 0.175 0.287 0.68↓ (±0.25) 0.251 1.000 0.222
J EST H63361 12q24.31 3.50↑ (±2.03) 0.271 0.376 0.66↓ (±0.26) 0.520 1.000 0.632
J hypothetical protein BC017488 W93317 16q13 0.60↓ (±0.05) 0.006 0.192 0.80↓ (±0.24) 0.345 1.000 0.354
J PTOV1 prostate tumour over expressed gene 1 AA486332 19q13.33 0.63↓ (±0.08) 0.090 0.265 0.84↓ (±0.17) 0.618 1.000 0.581
J LOC286467: hypothetical protein LOC286467 R95805 Xq26.1 2.85↑ (±1.02) 0.293 0.400 0.85↓ (±0.42) 0.530 1.000 0.716
  1. Genes are sorted by functional classification. A: Cellular metabolism (GO:0044237), Metabolism (other than energy metabolism), C: Nucleic acid binding (GO:0003676), D: Transcription regulator activity (GO:0030528), E: Signal transducer activity (GO:0004871), Signal transduction (GO:0007165) and Cell communication (GO:0007154), F: Cellular macromolecule metabolism (GO:0044260), G: Inflammatory response (GO:0006954), H: Organelle organization and biogenesis (GO:0006996I), I: Transport (GO:0006810), J: Biological process unknown (GO:0000004), Upward arrow denotes up-regulated mRNA expression, downward arrow down-regulated mRNA expression, bold indicates genes that have significant alteration in gene expression. Ratio is mean value calculated from three separate microarray experiments; SD is the standard deviation between separate experiments. Statistic probability (p-value) for TGFβ-treated vs. control and for IMR-treated vs. control, were calculated by using t-test. FDR is the calculated Benjamin-Hochberg false discovery rate. All three groups, TGFβ-treated, IMR-treated and control, were compared together with ANOVA.
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