Table 1.

Down-regulation of gene expression by N-myc

Tag sequence	Ratio *	SHEP2 ^†	SHEP21N ^†	P^‡	Unigene	Gene	Description
Cytoskeleton
GTTTCTAATA	10	5.8	0.6	0.006	31095	MAP4	Microtubule-associated protein 4
TGCTACGAAA	10	5.8	0.6	0.006	146550	MYH9	Myosin, heavy polypeptide 9, nonmuscle
TGCTAAAAAA	5	35.1	7.5	0.000	146550	MYH9	Myosin, heavy polypeptide 9, nonmuscle
TTAAAGATTT	9	26.5	2.9	0.000	133892	TPM1	Tropomyosin 1 (α)
ACAGGCTACG	9	11.2	1.2	0.000	410977	TAGLN	Transgelin
TGTAGAAAAA	7	8.5	1.2	0.001	512712	TUBB	Tubulin, β polypeptide
TCCAAATCGA	6	6.7	1.2	0.008	435800	VIM	Vimentin
AAGAGGTTTG	5	8.5	1.7	0.004	74368	CKAP4	Cytoskeleton-associated protein 4
GGTTAATTGA	>4	4	0	0.007	14376	ACTG1	Actin, γ 1
TAATATTTTT	4	11.7	2.9	0.002	443619	ACTN4	Actinin, α 4
CCCTTAGCTT	4	13.5	3.5	0.001	233936	MRCL3	Myosin regulatory light chain MRCL3
GCTTTATTTG	3	31.9	9.9	0.000	426930	ACTB	Actin, β
AACTGCTTCA	2	25.6	10.5	0.001	433506	ARPC1B	Actin-related protein 2/3 complex, subunit 1B, 41 kDa
TGTACCTGTA	2	28.3	11.6	0.001	446608	K-ALPHA-1	Tubulin, α, ubiquitous
CTGCCAAGTT	2	20.7	8.7	0.004	75873	ZYX	Zyxin
ECM structural
ATCTTGTTAC	22	13.5	0.6	0.000	418138	FN1	Fibronectin 1
TGCAATATGC	>12	11.7	0	0.000	750	FBN1	Fibrillin 1 (Marfan syndrome)
TTAAATAGCA	11	6.7	0.6	0.002	172928	COL1A1	Collagen, type I, α 1
TGGAAATGCC	8	13.9	1.7	0.000	172928	COL1A1	Collagen, type I, α 1
TTCGGTTGGT	5	20.2	4.1	0.000	172928	COL1A1	Collagen, type I, α 1
GGAGGAGAGC	>5	4.9	0	0.003	172928	COL1A1	Collagen, type I, α 1
TGGAAATGAC	5	85.9	15.7	0.000	172928	COL1A1	Collagen, type I, α 1
TGAAATTGTC	>4	4.5	0	0.004	172928	COL1A1	Collagen, type I, α 1
ACCAAAAACC	2	42.7	23.2	0.002	172928	COL1A1	Collagen, type I, α 1
GACCGCAGGA	11	6.7	0.6	0.002	437173	COL4A1	Collagen, type IV, α 1
ACAGATTTGA	>9	9.4	0	0.000	114599	COL8A1	Collagen, type VIII, α 1
TAAAAACAAA	9	5.4	0.6	0.010	114599	COL8A1	Collagen, type VIII, α 1
TAATCCTCAA	7	15.3	2.3	0.000	413175	COL18A	Collagen, type XVIII, α 1
TCTTGATATT	>5	5.4	0	0.004	283393	COL5A2	Collagen, type V, α 2
ECM regulator
TTTGCACCTT	58	35.1	0.6	0.000	410037	CTGF	Connective tissue growth factor
ATGTGAAGAG	22	539	25	0.000	111779	SPARC	Secreted protein, acidic, cysteine-rich (osteonectin)
AAAAAGCTGC	>15	14.8	0	0.000	111779	SPARC	Secreted protein, acidic, cysteine-rich (osteonectin)
GGTGGACACG	>12	12.1	0	0.000	111779	SPARC	Secreted protein, acidic, cysteine-rich (osteonectin)
CTAAAAACCT	>9	9.4	0	0.000	111779	SPARC	Secreted protein, acidic, cysteine-rich (osteonectin)
TTAGTGTCGT	8	9.9	1.2	0.000	111779	SPARC	Secreted protein, acidic, cysteine-rich (osteonectin)
TAAAAATGTT	8	35.1	4.6	0.000	119000	PAI1	Plasminogen activator inhibitor type 1
TCTCTGATGC	3	25.2	8.1	0.000	6441	TIMP2	Tissue inhibitor of metalloproteinase 2
Extracellular
CTTTCTTTGA	>8	7.6	0	0.000	130865	DKK3	DKK3 dickkopf homologue 3 (Xenopus laevis)
GTTTTTTTTA	6	10.3	1.7	0.001	437656	LEPRE1	Leucine proline-enriched proteoglycan (leprecan) 1
CATTATAACT	13	7.6	0.6	0.001	84359	DULLARD	Dullard homologue (Xenopus laevis)
AAGGAAATGA	>4	4.5	0	0.004	484063	SLIT3	Slit homologue 3 (Drosophila)
CATATCATTA	>15	14.8	0	0.000	435795	IGFBP7	Insulin-like growth factor binding protein 7
GCCCCAATAA	>10	10.3	0	0.000	407909	LGALS1	Lectin, galactoside-binding, soluble, 1 (galectin 1)
Signal transduction
AAGCCTTGCT	9	5.4	0.6	0.010	411366	GRB2	Growth factor receptor-bound protein 2
TCCGTGGTTG	>8	7.6	0	0.000	511745	BASP1	Brain abundant, membrane attached signal protein 1
TCTCAATTCT	4	12.6	2.9	0.001	146409	CDC42	Cell division cycle 42 (GTP binding protein, 25 kDa)
TCCTGTAAAG	4	14.4	4.1	0.001	74034	CAV1	Caveolin 1, caveolae protein, 22 kDa
AGCAGATCAG	2	26.5	11	0.001	143873	S100A10	S100 calcium binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11))
Integral to membrane
TGGCCTAATA	43	25.6	0.6	0.000	1501	SDC2	Syndecan 2 (heparan sulfate proteoglycan 1)
TGGCCTAAAA	>4	4.5	0	0.004	1501	SDC2	Syndecan 2 (heparan sulfate proteoglycan 1)
TACAATAAAC	11	13	1.2	0.000	9071	PGRMC2	Progesterone receptor membrane component 2
AGTTTCCCAA	10	12.1	1.2	0.000	279929	HSGP25L2G	gp25L2 protein
TCTTCTGCCA	6	9.4	1.7	0.002	86392	KIAA1402	CSGlcA-T KIAA1402 protein
TTCCTCCTTT	>7	7.2	0	0.000	151155	TM6SF1	Transmembrane 6 superfamily member 1
TTACTTATAC	>6	6.3	0	0.000	159	TNFRSF1A	Tumor necrosis factor receptor superfamily, member 1A
TAAGAAAATG	>6	5.8	0	0.001	443435	CDH11	Cadherin 11, type 2, OB-cadherin (osteoblast)
AGAACCTTAA	>5	4.9	0	0.003	181244	HLA-A	Major histocompatibility complex, class I, A
GCCCTTTCTC	3	25.2	7.5	0.000	7835	MRC2	Mannose receptor, C type 2
GTTGTGGTTA	2	60.3	28.5	0.000	75415	B2M	β-2-microglobulin
Transcription
TACAGAGGGA	8	9.4	1.2	0.000	406096	ZNF216	Zinc finger protein 216
AAAAGATACT	6	7.6	1.2	0.003	82071	CITED2	Cbp/p300-interacting transactivator, with Glu/Asp-rich COOH-terminal domain, 2
GCCATATTAT	>5	5.4	0	0.002	170752	CRIM1	Cysteine-rich motor neuron 1
CTCGAATAAA	>4	4.5	0	0.004	34871	ZFHX1B	Zinc finger homeobox 1b
Others
AATTTTCATT	10	5.8	0.6	0.006	339024	LOC253827	Hypothetical protein LOC253827
TTTTGTATTT	10	5.8	0.6	0.006	439190	C14orf31	Chromosome 14 open reading frame 31
GGTGAAGACA	7	8.5	1.2	0.001	26951	RUSC2	RUN and SH3 domain containing 2
CCCTGATTTT	6	19.8	3.5	0.000	183684	EIF4G2	Eukaryotic translation initiation factor 4 γ, 2
ATGTGAAGAA	6	6.7	1.2	0.008	13662	MGC5508	Hypothetical protein MGC5508
GAATAAATGT	6	7.2	1.2	0.005	497972	FKBP9	FK506 binding protein 9, 63 kDa
GCTGTTTTGT	>6	6.3	0	0.000	426312	AMOTL2	Angiomotin like 2
TTCCGGTTCC	5	9	1.7	0.003	172609	NUCB1	Nucleobindin 1
GTGGCTGAAA	>5	4.9	0	0.003	401929	rpL10	ribosomal protein L10
CTTAATCCTG	4	30.6	8.1	0.000	298275	SLC38A2	Solute carrier family 38, member 2
GAAATAATGG	4	18.4	4.6	0.000	343879	SPANXC	SPANX family, member C
AAGGCAATTT	4	12.6	2.9	0.001	301626	FLJ11739	Homo sapiens cDNA FLJ11739 fis
AAGTGAAACA	4	10.3	2.9	0.006	93659	ERP70	Protein disulfide isomerase related protein (calcium-binding protein, intestinal-related)
TTAAAACAAA	>4	4	0	0.01	370610	WAC	WW domain containing adaptor with coiled coil
AAAACATTCT	2	67.5	32.5	0.00	323562	DKFZp564K142	DKFZp564K142 implantation-associated protein

↵* Fold down-regulation of SHEP-2/SHEP-21N.
↵† The expression in SHEP-2 and SHEP-21N is given in number of tags normalized per 20,000 tags.
↵‡ Ps were calculated with the Monte Carlo simulation of the SAGE software ( 40).