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

Kati M Juuti-Uusitalo; Katri Kaukinen; Markku Mäki; Jarno Tuimala; Heikki Kainulainen

doi:10.1186/1471-2164-7-279

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

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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