Identification of differently expressed genes in human colorectal adenocarcinoma

Table 1 QRT-PCR parameters

Gene	Primer	Sequence	Length of primer (bp)	Length of product (bp)	Location of product
HSE1
	Forward prime	5’-TGGCAGGACAAGCGTTTAGA-3’	20	66	43–108
	Reverse prime	5’-CAGCACTCCTTTCAACCAATACTC-3	24
	TaqMan probe	5’>FAM AGTTTCTTCCACTCTTTG Quencher < 3’	18		64–81
SOX9
	Forward prime	5’-AGCGACGTCATCTCCAACATC-3’	21	49	1235–1
	Reverse prime	5’-GTTGGGCGGCAGGTACTG-3’	18		252
	TaqMan	5’>FAM CCTTCGATGTCAACGAGT Quencher < 3’	18
CaM					3098–3
	Forward prime	5’-GTTGAGCGAGGCAAATGGAT-3’	20	62	161
	Reverse prime	5’-TCCTTGGCAACAGTGCATCA-3’	20
	TaqMan	5’>FAM TCGATATTTCAGATGGGC Quencher <3 ’	18
β-Actin					1058–1
n	Forward prime	5’-CTGGCACCCAGCACAATG-3’	18	93	075
	Reverse prime	5’-GGACAGCGAGGCCAGGAT-3’	18
	TaqMan	5’>FAM ATCATTGCTCCTCCTGAG Quencher < 3’	18

Table 2 Differently expressed genes in subtracted cDNA populations

	Name of gene	Accessionnumber	cDNA	cDNA array ratio
				Group 1	Group 2
Proto-oncogene and tumor suppressor genes	ITGA6: integrin, alpha 6	ck570352	C60		2.277
Ion channels	ATP1B1: ATPase, Na+/K+ transporting, beta 1	ck570329	C8		0.352
proteins	polypeptide	ck570304,	a50	3.265
	CALM1: calmodulin 1 (phosphorylase kinase, delta)	ck570314	b19	1.856	0.344
Cell cycle proteins	PTMA: prothymosin, alpha	ck570346	C47		2.090
	BTG1: B-cell translocation gene 1, anti-proliferative	ck570300	a21	2.058
	DKFZp451J0118: taxilin
	CAPZA1: capping protein (actin filament) muscle	ck570339	c32		0.472
	Z-line, alpha 1	ck570343	c41		0.493
	TBDN100: transcriptional coactivator tubedown-100	ck570351	c58		2.211
Cell frame and movement	K-ALPHA-1: tubulin, alpha, ubiquitous	ck570353	C61		2.281
	TUBB2: tubulin, beta, 2	ck570366	C91		3.21
	CAPZA1: capping protein (actin filament) muscle Z-line, alpha 1	ck570343	C41		0.493
Apoptosis related proteins Signal	K-ALPHA-1: tubulin, alpha, ubiquitous	ck570339	C32		0.472
	SRPRB: signal recognition particle receptor, B subunit	ck570312	b12	1.540	0.425
transmitting related proteins	PERQ1: PERQ amino acid rich, with GYF domain 1	ck570299	a15	0.486
Synthesis and translation	ZNF403: zinc finger protein 403	ck570360	C85	3.197	3.197
related proteins	SOX9: SRY (sex determining region Y)-box 9	ck570305,	b2	0.426	2.344
	(campomelic dysplasia, autosomal sex-reversal)	ck570306,	b3	0.489	1.593
		ck570361	c86		3.391
	SET: SET translocation (myeloid leukemia-associated)	ck570344	c43		2.447
	Bit1: Bcl-2 inhibitor of transcription
	EIF3S6: eukaryotic translation initiation factor 3, subunit	ck570355	c73		2.666
	6 48 KD	ck570311	b11	0.660	2.091
	EIF4E: eukaryotic translation initiation factor 4E
	NCL: nucleolin	ck570336	c16		0.392
		ck570367	c92		4.67
Metabolism	RPL7: ribosomal protein L7	ck570290	a3	0.359
related proteins	RPS24: ribosomal protein S24	ck570297	a13	0.457
	RPS25: ribosomal protein S25	ck570349	c55		2.202
	COX7C: cytochrome c oxidase subunit VIIc	ck570315	b20	1.860	0.580
	FABP1: fatty acid binding protein 1, liver	ck570324	b39	2.807	0.547
	SAT: spermidine/spermine N1-acetyltransferase	ck570335	c13		0.375
	SCD: stearoyl-CoA desaturase (delta-9-desaturase)	ck570357	c81		3.098
	PAFAH1B2: platelet-activating factor acetylhydrolase, isoform Ib, beta subunit 30 KD protein 1	ck570292	a7	0.421
Immunity and stimulation related proteins	HSPE1: heat shock 10 protein 1 (chaperonin 10)	ck570307,	b6	0.562	3.191
		ck570308,	b7	0.567	2.686
		ck570310,	b9	0.649	2.532
		ck570347	c52		2.132
	HSPD1: heat shock 60 KD protein 1 (chaperonin)	ck570356	c77		2.786
	IGHG1: immunoglobulin heavy constant gamma 1	ck570363	c90		4.667
	(G1m marker)	ck570321	b5-1	0.493	2.830
	IFITM3: interferon induced transmembrane protein 3 (1–8 U)	ck570309	b8	0.634	3.021
	PSMA7: proteasome (prosome, macropain) subunit, alpha type, 7
Cell receptor	PIGR: polymeric immunoglobulin receptor	ck570301,	a28	2.309
		ck570303,	a39	2.552
		ck570313,	b13	1.554	0.330
		ck570316,	b21	1.869	0.505
		ck570318,	b24	1.982	0.394
		ck570319	b40	2.942	0.662
Others	C6orf62: chromosome 6 open reading frame 62	ck570289	a2	0.236
	IRA1: likely ortholog of mouse IRA1 protein	ck570291	a4	0.402
	MRNA: cDNA DKFZp686P07216 (from clone DKFZp686P07216)	ck570296	a12	0.450
	DACH1: dachshund homolog 1 (Drosophila)	ck570298	a14	0.482
	TXNIP: thioredoxin interacting protein	ck570317	b23	1.959	0.297
	LOC376745: AG1	ck570328	c5		0.336
	Transcribed sequence with strong similarity to protein prf:0512543A (H. sapiens) 0512543A oxidase II, cytochrome	ck570333	c12		0.373
	C14orf112: chromosome 14 open reading frame 112	ck570337	c19		0.414
	Transcribed sequence with moderate similarity to	ck570348	c53		2.152
	protein sp:P18124 (H. sapiens) RL7_HUMAN 60S	ck570354	c71		2.648
	ribosomal protein L7	ck570358	c82		3.127
	F LJ32421: hypothetical protein FLJ32421	ck570364,	c50		2.104
	C20orf45: chromosome 20 open reading frame 45	ck570322,	b38	2.665	0.368
		ck570327,	b44	2.942	0.590
	CDNA clone MGC:62026 IMAGE:6450688, complete cds	ck570330,	c10		0.368