BioMed Research International

Research Article

Characteristic Gene Expression Profiles of Human Fibroblasts and Breast Cancer Cells in a Newly Developed Bilateral Coculture System

Table 5

(a) Enrichment analysis: common changes in breast cancer cells. (b) Enrichment analysis: common changes in breast cancer cells. (c) Genes of altered expression in breast cancer cells cocultured with fibroblast.

(a)


#	Upregulation: GO processes in common of MCF7, SKBR3, and HCC1937 (104 genes)	value	FDR

1	Cell cycle
	D53, CDC18L (CDC6), ECT2, MCM7, Bard1, Thymidylate kinase, TTK, Rabkinesin-6, VRK1, HDAC1, TIPIN, CDC20, Histone deacetylase class I, DCC1, RFC4, ORC6L, CD2AP, EXO1, and BORIS

2	Mitotic cell cycle
	D53, CDC18L (CDC6), MCM7, TTK, Rabkinesin-6, VRK1, HDAC1, TIPIN, CDC20, Histone deacetylase class I, DCC1, RFC4, ORC6L, CD2AP, C15orf23, HSP70, MAD2a, PBK, and TOP2 alpha

3	Cell cycle process
	D53, CDC18L (CDC6), ECT2, MCM7, Bard1, TTK, Rabkinesin-6, VRK1, TIPIN, CDC20, Histone deacetylase class I, DCC1, RFC4, ORC6L, CD2AP, C15orf23, HSP70, MAD2a, PBK, and TOP2 alpha

4	Mitotic cell cycle process
	D53, CDC18L (CDC6), MCM7, TTK, VRK1, TIPIN, CDC20, DCC1, ORC6L, CD2AP, C15orf23, HSP70, MAD2a, PBK, TOP2 alpha, Tubulin alpha, RRS1, Aurora-A, MSH2, CDK inhibitor 3, CKS1, and Tome-1

5	Cell division
	CDC18L (CDC6), ECT2, Rabkinesin-6, VRK1, TIPIN, CDC20, DCC1, CD2AP, EXO1, C15orf23, HSP70, MAD2a, PBK, TOP2 alpha, Tubulin alpha, RRS1, Aurora-A, MSH2, CKS1, Tome-1, and CCAR1

#	Upregulation: metabolic networks in common of MCF7, SKBR3, and HCC1937 (104 genes)	value	FDR

1	Carbohydrate metabolism_TCA and tricarboxylic acids transport
	ODO2, SLC25A21, and SUCB1

2	Carbohydrate metabolism_propionate metabolism and transport
	ACAT2, ACYP1, and SUCB1

3	Amino acid metabolism_lysine metabolism and transport
	ODO2, ACAT2

4	Phosphatidylcholine pathway
	HSP70, COASY

5	1,2-Didocosapentaenoyl-sn-glycerol_3-phosphate pathway
	AP3D1, Tubulin alpha

(b)


#	Downregulation: GO processes in common of MCF7, SKBR3, and HCC1937 (105 genes)	value	FDR

1	Negative regulation of vasoconstriction
	HSPA1A, HSPA1B, HSP70, and HIF1A

2	Positive regulation of erythrocyte differentiation
	HSPA1A, HSPA1B, ID2, HSP70, and HIF1A

3	Response to mechanical stimulus
	ITGB1, EGR1, KV1.5, JunB, HSPA1A, HSPA1B, p70 S6 kinases, HSP70, c-Fos, ASNS, and HIF1A

4	Response to radiation
	AKR1C4, ITGB1, EGR1, AKR1C1, Catalase, JunB, HSPA1A, HSPA1B, HSP70, PUMA, DEC1 (Stra13), USP47, c-Fos, ASNS, and HIF1A

5	Protein refolding
	HSPA1A, HSPA1B, ST13 (Hip), and HSP70

#	Downregulation: metabolic networks in common of MCF7, SKBR3, and HCC1937 (105 genes)	value	FDR

1	Phosphatides acid pathway
	PPAP2, LPP3

2	D-Glucuronic acid pathway
	AKR1C4, TBP, and c-Fos

3	Steroid metabolism_pregnenolone and progesterone metabolism
	AKR1C4, HSD17B8, and AKR1C2

4	2-Arachidonoylglycerol_3-phosphocholine pathway
	Tissue kallikreins, Prostasin, and HIF1A

5	(L)-Leucine pathways and transport
	p70 S6 kinase2, OSCP1

(c)


Upregulated genes			Downregulated genes
MCF7	SKBR3	HCC1937	MCF7	SKBR3	HCC1937

IFIT1	PTGS1	BUB1	STK19	DUSP1	SCGB1A1
AP1B1	CTSZ	CDCA8	HMOX1	FOS	TF
OAT	CYP1B1	C13orf34	MEIS3	EGR1	C20orf114
ECT2	ALDH3B2	ABHD10	NMT1	SYCE1	LYNX1
EFNA1	SFRS16	NSMAF	CRK	NUPR1	CLCA2
TMEM189-UBE2V1	BPNT1	KIF2C	DIABLO	NR4A2	CASP14
AMH	SLC39A7	SREBF2	WDR34	ENDOD1	CP
NFE2L2	ATF1	SLC20A1	D2HGDH	NR4A1	EGLN3
PDPK1	A4GNT	EBNA1BP2	ATP1B1	OR14K1	C7orf29
HSPA8	BLZF1	NCAPH	TIMM50	ATF4	MATN2
ZNF117	TUBA3C	TFPI2	TMEM183A	IFI6	SERPINA3
GM2A	EXO1	PHLDA1	GDI1	BAK1	TNFSF10
NUF2	ST3GAL4	ATP6V1C1	TMEM168	ASNS	TMC4
ANP32A	CSNK2A1	DDX47	COX7B	SCNM1	ANGPTL4
ACYP1	CARHSP1	ODC1	AIFM2	TPM4	LY6D
RCN2	C13orf37	VEGFC	NUP188	MXD1	S100A8
STX3	TRAF4	GTF2B	DUSP22	ACTA1	CHI3L2
TSSC1	C4orf43	SLC10A3	MAK16	CTGF	KRT15
HEBP1	DCTPP1	ALDH7A1	TROAP	MED13	PSCA
FAM132A	CCAR1	CDC45L	C19orf46	ZNF783	SELENBP1
TMED10	BAX	FUBP1	MED13	CXorf23	NUPR1
KTN1	DSCC1	GS1-484O17.2	CLDN4	ADM	ANKRD37
ACTR6	YWHAG	CCT8	SLC25A1	SREBF2	CLDN8
AURKA	TEX261	MEST	ARF1	ID1	FBXO32
NGRN	S100A9	NCAPG	PHF2	ZG16	PLXND1
ILK	FAM10A5	MKI67	FFAR3	RGS16	SERPINA5
STAT1	FKBP10	KIAA0101	SCAF1	CLIC4	FOS
PWP1	ACO2	SUB1	C2orf76	MED12	NDRG1
PABPC3	TMSB4X	KIAA1524	MYOM2	JUN	CRIP2
SLBP	VWA5B1	FGF2	KCTD17	RNF126	WFDC2