Identification of osteopontin as the most consistently over-expressed gene in intrahepatic cholangiocarcinoma: Detection by oligonucleotide microarray and real-time PCR analysis

Table 3 Most significantly dysregulated genes (> 4-fold change in 100% of all cases) in intrahepatic cholangiocarcinoma - relation to known cellular functions and metabolic pathways (using the GenMAPP^® software)

Swiss prot	GenMAPP ID	Gene ID	Dysregulated in %	Name	fc inc (median)	fc dec (median)
Cell adhesion (cell-cell/cell-matrix)-extracellular matrix
OSTP_HUMAN	P10451	SPP1	100	Osteopontin precursor (Bone sialoprotein 1/SPP-1 1)	33.5
Q13443	Q13443	ADAM9	100	A disintegrin and metalloproteinase domain 9 (meltrin γ)	10.4
TYBO_HUMAN	P13472	TMSB10	100	Thymosin beta-10	5.3
ITA6_HUMAN	P23229	ITGA6	100	Integrin alpha-6 precursor	4.5
Signal transduction - G protein signaling
CD24_HUMAN	P25063	CD24	100	Signal transducer CD24 precursor	11.8
IQG1_HUMAN	P46940	IQGAP1	100	Ras GTPase-activating-like protein IQGAP1	9.1
ECT2_HUMAN	Q9H8V3	ECT2	100	ECT2 protein (Epithelial cell transforming 2 oncogene)	6.3
MACS_HUMAN	P29966	MACS	100	Myristolated alanine-rich C-kinase substrate (MARCKS)	4.6
Q9BUV5	Q9BUV5	INSIG1	100	Similar to insulin induced gene 1		5
Cell cycle - DNA replication
RIR2_HUMAN	P31350	RRM2	100	Ribonucleoside-diphosphate reductase M2 chain	16.2
S111_HUMAN	P31949	S100A11	100	Calgizzarin (S100C protein)	15.5
O00496	O00496	IPL	100	Tumor suppressing subtransferable candidate 3	14.1
S106_HUMAN	P06703	S100A6	100	Calcyclin (Growth factor inducible protein 2A9)	6.9
Transcription
SOX9_HUMAN	P48436	SOX9	100	Transcription factor SOX9	4.1
NRI3_HUMAN	Q14994	NR1/3	100	Orphan nuclear receptor NR1/3		6.8
Cell motility – cytoskeleton
SPT2_HUMAN	O53291	SPINT2	100	Kunitz-type protease inhibitor 2 precursor (Hepatocyte growth factor activator inhibitor type 2)	5.8
Amino acid metabolism
BHMT_HUMAN	Q93088	BHMT	100	Betaine-homocysteine S-methyltransferase		48.5
METL_HUMAN	Q00266	MAT1A	100	S-adenosylmethionine synthetase alpha and beta forms		38.5
ATTY_HUMAN	P17735	TAT	100	Tyrosine aminotransferase		27.0
SPYA_HUMAN	P21549	AGXT	100	Serine-pyruvate aminotransferase		22.0
HUTH_HUMAN	P42357	HAL	100	Histidine ammonia-lyase		16.7
CGL_HUMAN	P32929	CTH	100	Cystathione gamma-lyase (Gamma-Cystathionase)		9.9
GLSL_HUMAN	Q9UI32	GA	100	Glutaminase, liver isoform, mitochondrial precursor		9.5
GAMT_HUMAN	Q14353	GAMT	100	Guanidinoacaetate N-methyltransferase		8.4
SDHL_HUMAN	P20132	SDS	100	L-serine dehydratase		7.1
Carbohydrate/monosaccharide metabolism/catabolism
KPY2_HUMAN	P14786	PKM2	100	Pyruvate kinase, M2 isozyme	26.7
ALFA_HUMAN	P04075	ALDOA	100	Fructose biphosphate aldolase A (Lung cancer antigen)	16.3
PPCC_HUMAN	Q16822	PCK1	100	Phosphoenolpyruvate carboxykinase, cytosolic		16.7
Q9H277	Q9H277	Q9H227	100	Cytosolic beta-glucosidase		7.6
Electron transport
ACDB_HUMAN	P45954	ACADSB	100	Acyl-CoA dehydrogenase, branched chain specific		14.1
CPA6_HUMAN	X13929	CYP2A6	100	Cytochrome P450 2A6		11.9
CP12_HUMAN	P05177	CYP1A2	100	Cytochrome P450 1A2		10.0
Protein metabolism/proteolysis
BAE2_HUMAN	Q9Y5Z0	BACE2	100	Beta secretase 2 precursor	10.5
Q9UJ28	Q9UJ28	GALNT7	100	UDP-GalNAc: N-acetylgalactosaminyltransferase 7	5.4
CATC_HUMAN	P53634	CTSC	100	Dipeptidyl-peptidase I precursor	4.7
GLMT_HUMAN	Q14749	GNMT	100	Glycine N-methyltransferase		49.5
Transport
CHLR_HUMAN	P17516	AKR1C4	100	Chlordecone reductase		22.0
APF_HUMAN	Q13790	APOF	100	Apolipoprotein F precursor		15.5
Lipid binding/metabolism
Q9Y2P5	Q9Y2P5	Q9Y2P5	100	Very-long-chain AcylCoA synthetase homolog 2		23.7
VLCS_HUMAN	O14975	FACVL1	100	Very-long-chain AcylCoA synthetase		16.6
MMSA_HUMAN	Q02252	MMSDH	100	Methylmalonate-semialdehyde dehydrogenase		8.1