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Table 1 List of affected genes that had a significant change in their mRNA expression when TGFβ-differentiated T84 cells were compared to T84 cells grown solely in collagen I gel (= TGFβ-treated vs. control) and T84 cells differentiated by soluble factors secreted by mesenchymal cells were compared to T84 cells grown solely in collagen I gel (= 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
     ratio SD p-value FDR ratio SD p-value FDR
A DHCR24: 24-dehydrocholesterol reductase AA482324 1p33-p31.1 0.68 (±0.20) 0.699 0.733 1.01 (±0.14) 0.969 1.000
A FDPS: farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) T66907
T65907
1q22 0.29↓
0.57↓
(±0.24)
(±0.45)
0.180
0.148
0.291
0.272
1.43
1.06
(±1.32)
(±1.02)
0.807
0.499
1.000
1.000
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
A CYP3A4: cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 4 R91078 7q21.1 0.70 (±0.05) 0.372 0.479 0.88 (±0.18) 0.520 1.000
A CYP2E: cytochrome P450, subfamily IIE (ethanol-inducible) H50500 10q24.3-qter 0.58 (±0.31) 0.509 0.607 0.96 (±0.60) 0.991 1.000
A CYP19A1: cytochrome P450, family 19, subfamily A, polypeptide 1 R32428 15q21.1 0.75 (±0.08) 0.744 0.812 1.09 (±0.14) 0.923 1.000
B SDHB: succinate dehydrogenase complex, subunit B, iron sulfur (Ip) AA463565 1p36.1-p35 0.43 (±0.20) 0.041 0.265 0.81 (±0.38) 0.570 1.000
B UQCR: ubiquinol-cytochrome c reductase (6.4 kD) subunit R46837 19p13.3 0.42 (±0.40 0.123 0.265 0.90 (±0.49) 0.629 1.000
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
D EIF4E2: eukaryotic translation initiation factor 4E member 2 W01534 2q37 3.54 (±1.90) 0.390 0.495 0.90 (±0.71) 0.499 1.000
D TFDP2: transcription factor Dp-2 AA465444 3q23 0.57 (±0.18) 0.036 0.265 0.97 (±0.33) 0.920 1.000
D HNRPH1: heterogeneous nuclear ribonucleoprotein H1 W96114 5q35.3 0.53 (±0.24) 0.572 0.665 0.98 (±0.39) 0.739 1.000
D ZNF193: zinc finger protein 193 AA252169 6p21.3 0.49 (±0.20) 0.102 0.265 0.96 (±0.68) 0.482 1.000
D MYC: v-myc myelocytomatosis viral oncogene homolog (avian) AA464600 8q24.12-q24.13 0.78 (±0.42) 0.156 0.275 0.91 (±0.27) 0.800 1.000
D PRP18: pre-mRNA processing factor 18 H82325 10p12.33 0.52 (±0.28) 0.086 0.265 0.97 (±0.22) 0.791 1.000
D TFDP1: transcription factor Dp-1 W33012 13q34 0.76 (±0.009) 0.858 0.898 0.99 (±0.26) 0.957 1.000
D EIF2B2: eukaryotic translation initiation factor 2B, subunit 2 (beta, 39 kD) R86304 14q24.3 0.64 (±0.19) 0.018 0.261 1.05 (±0.25) 0.765 1.000
D ZNF161: zinc finger protein 161 AA232647 17q23.3 0.710.75 (±0.11) (±0.13) 0.339 0.445 0.94 1.08 (±0.31) (±0.11) 0.608 1.000 1.000
D ZNF24: zinc finger protein 24 (KOX 17) AA447098 18q12 0.73 (±0.07) 0.651 0.732 1.10 (±0.46) 0.712 1.000
D ZNF358: Zinc finger protein 358 H20045 19p13 0.64 (±0.09) 0.304 0.411 0.93 (±0.30) 0.621 1.000
D MRPL4: mitochondrial ribosomal protein L4 AA490981 19p13.2 0.66 (±0.13) 0.030 0.265 0.90 (±0.16) 0.503 1.000
D RPS5: ribosomal protein S5 AA456616 19q13.4 0.66 (±0.13) 0.030 0.265 0.90 (±0.16) 0.503 1.000
D EZF-2: endothelial zinc finger protein 2 R63318 19q13.43 0.58 (±0.22) 0.061 0.265 0.87 (±0.23) 0.374 1.000
D ID1: inhibitor of DNA binding 1, dominant negative helix-loop-helix protein AA457158 20q11 0.74 (±0.18) 0.210 0.317 1.06 (±0.13) 0.807 1.000
D SF3A1 splicing factor 3a, subunit 1. 120 kD T72698 22q12.2 0.71 (±0.13) 0.510 0.609 1.11 (±0.36) 0.967 1.000
E CTNNBIP1: catenin, beta interacting protein 1 R78539 1p36.22 0.59 (±0.33) 0.205 0.313 1.23 (±0.91) 0.836 1.000
E CTNNB1: catenin (cadherin-associated protein), beta 1, 88 kDa AA442092 3p21 0.65 (±0.06) 0.628 0.712 0.99 (±0.08) 0.948 1.000
E WNT5A: wingless-type MMTV integration site family, member 5A W49672 3p21-p14 0.72 (±0.19) 0.307 0.414 1.07 (±0.16) 0.899 1.000
E TGFBR2: transforming growth factor, beta receptor II (70–80 kD) AA487034 3p22 0.71 (±0.17) 0.450 0.555 1.06 (±0.14) 0.906 1.000
E SIAH2: seven in absentia homolog 2 (Drosophila) AA029041 3q25 0.65 (±0.13) 0.037 0.265 1.01 (±0.19) 0.948 1.000
E PIK3R1: phosphoinositide-3-kinase, regulatory subunit, polypeptide 1 (p85 alpha) R54050 5q12-q13 0.61 (±0.11) 0.539 0.636 1.25 (±0.75) 0.832 1.000
E PDGFRB: platelet-derived growth factor receptor, beta polypeptide R56211 5q31-32 1.01 (±0.29) 0.957 0.973 1.23 (±0.16) 0.390 1.000
E EGFR: epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) R35665
W48713
7p12 0.470.75 (±0.04) (±0.13) 0.022 0.444 0.265 0.550 1.02 1.09 (±0.63) (±0.10) 0.806 0.693 1.000 1.000
E IGF2: insulin-like growth factor 2 (somatomedin A) N54596 11p15.5 0.570.63 (±0.16) (±0.17) 0.241 0.335 0.345 0.441 0.92 1.23 (±0.27) (±0.86) 0.565 0.912 1.000 1.000
E SIAH1: seven in absentia homolog 1 (Drosophila) AA447531 16q12 0.57 (±0.23) 0.055 0.265 0.97 (±0.55) 0.920 1.000
E NLK: nemo-like kinase R70769 17q11.2 0.55 (±0.24) 0.298 0.504 0.85 (±0.39) 0.499 1.000
E SMAD4: SMAD, mothers against DPP homolog 4 (Drosophila) AA456439 18q21.1 0.78 (±0.14) 0.186 0.296 1.00 (±0.23) 0.870 1.000
F CTSS: cathepsin S AA236164 1q21 0.53 (±0.04) 0.327 0.433 0.90 (±0.30) 0.580 1.000
F PSMA3: proteasome (prosome, macropain) subunit, alpha type, 3 AA465593 14q23 0.58 (±0.19 0.319 0.426 1.11 (±0.68) 0.700 1.000
F PSMB6: proteasome (prosome, macropain) subunit, beta type, 6 AA070997 17p13 0.76 (±0.16) 0.093 0.265 1.00 (±0.12) 0.972 1.000
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
H KRT19:keratin 19 AA464250 17q21.2 13.90 (±16.73) 0.390 0.496 19.95 (±12.99) 0.499 1.000
J LOC440582: similar to Peptidyl-prolyl cis-trans isomerase E (PPIase E) (Rotamase E) (Cyclophilin E) (Cyclophilin 33) W17246 1p34.3 0.79 (±0.20) 0.290 0.397 1.11 (±0.14) 0.293 1.000
J RP4-622L5: hypothetical protein RP4-622L5 T85191 1p36.11-p34.2 0.69 (±0.13) 0.066 0.265 1.11 (±0.37) 0.673 1.000
J EST T99671 2q36 0.66 (±0.18) 0.610 0.698 0.99 (±0.30) 0.770 1.000
J FLJ12057 N77990 3q21 0.71 (±0.10) 0.394 0.501 1.01 (±0.26) 0.840 1.000
J MGC2198 H81199 3q27-q28 0.57 (±0.25) 0.258 0.364 1.21 (±0.97) 0.727 1.000
J EST R74480 5 0.65 (±0.09) 0.148 0.272 0.93 (±0.55) 0.458 1.000
J CCL28: chemokine (C-C motif) ligand 28 R38459 5p12 0.63 (±0.13) 0.288 0.395 1.06 (±0.41) 0.905 1.000
J FCHO2: FCH domain only 2 H93842 5q13 1.03 (±0.54) 0.859 0.900 1.48 (±0.44) 0.277 1.000
J Hypothetical gene supported by AK126569 N92035 5q23 0.52 (±0.20) 0.161 0.277 0.94 (±0.31) 0.577 1.000
J SMG1: PI-3-kinase-related kinase SMG-1 W32907 6p12.3 0.70 (±0.22) 0.207 0.315 1.36 (±0.55) 0.259 1.000
J cDNA DKFZp667D095 R26163 8p22 0.61 (±0.32) 0.118 0.265 1.10 (±0.59) 0.857 1.000
J DPYS: hypothetical protein PRO2949 N73761 8q22 3.29↓ (±1.73) 0.513 0.611 0.85 (±0.54) 0.566 1.000
J D12S2489E AA397819 12p13.2-p12.3 0.66 (±0.06) 0.011 0.227 0.92 (±0.19) 0.678 1.000
J ZNF629: Zinc finger protein 629 AA128587 16p11.1 0.55 (±0.15) 0.157 0.275 0.93 (±0.33) 0.533 1.000
J cDNA FLJ32121 fis, clone PEBLM1000083 T69477 16q22 0.57 (±0.18) 0.124 0.265 0.85 (±0.25) 0.698 1.000
J SFRS14: splicing factor, arginine/serine-rich 14 AA485539 19p12 0.70 (±0.17) 0.201 0.310 1.88 (±1.38) 0.995 1.000
J PNPLA4: patatin-like phospholipase domain containing 4 AA449678 Xp22.3 0.58 (±0.09) 0.387 0.495 0.94 (±0.33) 0.634 1.000
J LOC286467: hypothetical protein LOC286467 R95805 Xq26.1 2.85↑ (±1.02) 0.293 0.400 0.85 (±0.42) 0.530 1.000
  1. Genes are sorted by functional classification. A: Cellular metabolism (GO:0044237), Metabolism (other than energy metabolism), B: Generation of precursor metabolites and energy GO:0006091), 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), 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, was calculated by using t-test. FDR is the calculated Benjamin-Hochberg false discovery rate.