Bioinformatic approach for understanding the heterogeneity of cholangiocytes

Table 1 Differences in cDNA expression between small and large cholangiocyte lines

GO1 annotation/ Gene name	Gene accession	GO accession	Small2	Large3	Ratio (L/S)
Immune response		GO:0006955
CD1d1 antigen	NM_007639		107	156	1.46
CD1d2 antigen	NM_007640		80	131	1.64
CD86 antigen; B7-2; CD28 antigen ligand 2 (CD28L2)	L25606		52	17	0.33
Histocompatibility 2, class II antigen E alpha	NM_010381		132	407	3.08
Histocompatibility 2, class II antigen A, beta 1	NM_010379		586	832	1.42
Histocompatibility 2, class II antigen E beta	NM_010382		3579	4481	1.25
Interleukin 2 receptor, beta chain	NM_008368		540	2604	4.83
Cell adhesion		GO:0007155
Intercellular adhesion molecule 1 (ICAM1)	X52264		39	20	0.51
Vascular cell adhesion molecule 1 (VCAM1)	M84487		17	11	0.65
Cadherin 1 (CDH1); epithelial cadherin (E-cadherin; E-CAD); uvomorulin (UM)	X06115		32	42	1.29
Cytoskeleton		GO:0005856
Cytoplasmic beta-actin (ACTB)	M12481		455	275	0.60
Vimentin (VIM)	X51438		260	73	0.28
Proteolysis		GO:0006508
Matrix metalloproteinase 14 (MMP14); membrane-type matrix matalloproteinase 1 (MTMMP1)	X83536		2585	1339	0.52
Cell death		GO:0008219
Fas antigen ligand (FASL); apoptosis antigen ligand (APTL; APT1LG1); tumor necrosis factor superfamily member 6 (TNFSF6); generalized lymphoproliferative disease protein (GLD)	U06948		37	21	0.57
Fas antigen; fasL receptor; apoptosis antigen 1 (APO1; APT1); CD95 antigen	M83649		18	20	1.07
Fas death domain-associated protein	NM_007829		392	103	0.26
Fas-associating protein with death domain	NM_010175		484	188	0.39
B-cell leukemia/lymphoma protein 2 (BCL2)	M16506		31	18	0.56
Caspase 9	NM_015733		318	996	3.14
Anti-apoptosis
Insulin-like growth factor 1 receptor alpha subunit (IGFIR-alpha)	U00182	GO:0006916	95	176	1.86
Inflammatory response		GO:0006954
Tumor necrosis factor	NM_013693		130	275	2.11
Tumor necrosis factor (ligand) superfamily, member 4	NM_009452		98	227	2.32
Tumor necrosis factor (ligand) superfamily, member 7	NM_011617		133	239	1.80
Tumor necrosis factor (ligand) superfamily, member 8	NM_009403		189	514	2.73
Tumor necrosis factor (ligand) superfamily, member 9	NM_009404		278	305	1.10
Tumor necrosis factor (ligand) superfamily, member 19	NM_011615		164	88	0.53
Tumor necrosis factor receptor superfamily member 1A (TNFRSF1A); tumor necrosis factor receptor 1 (TNFR1)	X57796		58	41	0.72
Tumor necrosis factor receptor superfamily member 1B2 (TNFRSF1B2); tumor necrosis factor receptor 2 (TNFR2)	M59378		18	17	0.92
Interleukin 6 receptor alpha subunit (IL6R-alpha; IL6RA)	X51975		57	64	1.13
Cytokine activity		GO:0005125
Interleukin 6 (IL6)	X06203		36	25	0.70
Oncostatin M (OSM)	D31942		79	509	6.42
Cellular metabolism		GO:0044237
PDC-E2			NT	NT
PDC-E3BP			NT	NT
Transport		GO:0006810
Solute carrier family 4 (anion exchanger), member 2	NM_009207		80	145	1.82
Solute carrier family 4 (anion exchanger), member 3	NM_009208		52	120	2.31
Solute carrier family 4 (anion exchanger), member 1	NM_011403		995	2146	2.16
Voltage-dependent anion channel 1	NM_011694		111	146	1.32
Voltage-dependent anion channel 2	NM_011695		87	62	0.71
Solute carrier family (organic anion transporter) member 1	NM_013797		76	114	1.50
Aquaporin 1	NM_007472		257	245	0.95
Aquaporin 2	NM_009699		198	276	1.39
Aquaporin 3	NM_016689		124	204	1.64
Aquaporin 5	NM_009701		396	222	0.56
Aquaporin 8	NM_007474		2160	8728	4.04
Solute carrier family 10 (sodium/bile acid cotransporter family), member 1	NM_011387		208	402	1.93
G-protein coupled purinergic receptor P2Y1 (P2RY1)	U22829		346	652	1.89
Purinergic receptor P2X, ligand-gated ion channel 4	NM_011026		711	2229	3.13
Detection of Stimulus		GO0051606
Toll-like receptor 2	NM_011905		95	68	0.72
Toll-like receptor 5	NM_016928		168	114	0.68
Toll-like receptor 6	NM_011604		255	569	2.23
Cell proliferation		GO:0008283
FMS-like tyrosine kinase 1 (FLT1); vascular endothelial growth factor receptor 1 (VEGFR1)	L07297		36	23	0.65
Epidermal growth factor (EGF)	J00380		88	116	1.32
Kinase insert domain receptor (KDR); vascular endothelial growth factor receptor 2 (VEGFR2); FLK1	X70842		93	58	0.62
Vascular endothelial growth factor (VEGF); vascular permeability factor (VPF)	M95200		165	152	0.92
Heparin-binding growth factor 5 (HBGF5); fibroblast growth factor 5 (FGF5)	M30643		355	152	0.43
Fibroblast growth factor receptor 3 (FGFR3); heparin-binding growth factor receptor (HBGFR)	M81342		192	485	2.53
Transforming growth factor beta 1 (TGF-beta 1; TGFB1)	M13177		69	105	1.51
Transforming growth factor beta receptor 1 (TGF-beta receptor 1; TGFR1); ESK2	D25540		44	29	0.65
Acetylcholine receptor M3	NM_033269		NT	NT
Cell cycle		GO:0007049
Proliferating cell nuclear antigen (PCNA); cyclin	X53068		211	124	0.59
Cell growth
Estrogen receptor 1 (ESTR1); estrogen receptor alpha (ER-alpha; ESTRA)	M38651	GO:0016049	22	33	1.48
Others
Nerve growth factor receptor	AF105292	GO:0007411	N.T.	N.T.
Neurotrophic tyrosine kinase receptor type1	XM283871	GO:0042490	N.T.	N.T.
Neurotrophic tyrosine kinase receptor type 2	M33385	GO:0042490	93	18	0.20
Neurotrophic tyrosine kinase, receptor, type 3	NM_008746	GO:0042490	2923	3827	1.31
Interferon gamma receptor (IFN-gamma receptor; IFNGR)	M28233	GO:0005615	51	50	0.98

The entire dataset obtained from the Atlas Glass Array mouse (Clontech, Takara Bio Inc., Shiga, Japan) was analyzed by ArrayGauge software (Fuji Photo Film Co., Ltd., Tokyo).

¹gene ontology, ^2,3spot intensities of all samples from small or large cholangiocytes.