Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach

Lu, Jun; Tomfohr, John K; Kepler, Thomas B

doi:10.1186/1471-2105-6-165

BMC Bioinformatics

Table 6 A list of top 40 genes differentially expressed between pancreatic cancer and normal ductal epithelium

From: Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach

Tag	Description	P	HX	H126	ASPC	PL45	CAPAN1	CAPAN2	Panc-1
Up-regulated in pancreatic cancer
CTTCCAGCTA	annexin A2	0.0011	19	25	128	217	143	148	170
AAAAAAAAAA	-	0.0018	6	3	128	210	180	165	133
AGCAGATCAG	S100 calcium binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11))	0.0027	16	9	272	152	138	135	384
TTGGTGAAGG	thymosin, beta 4, X-linked	0.003	6	0	90	267	194	187	238
CCCATCGTCC	motichondria gene	0.0032	13	34	2047	1333	364	456	408
CCTCCAGCTA	keratin 8	0.0059	3	16	452	1766	292	265	364
GGAAAAAAAA	ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit	0.0063	3	6	64	61	74	74	57
CCCCAGTTGC	calpain, small subunit 1	0.0066	22	22	64	88	77	61	113
AACTAAAAAA	ribosomal protein S27a	0.0078	19	16	45	85	80	61	61
TTCAATAAAA	RPLP1, Ribosomal protein, large, P1	0.0079	9	25	147	179	135	104	40
GCAAAAAAAA	chromosome 21 open reading frame 97	0.0079	6	3	58	68	40	65	65
ACTTTTTCAA	motichondria gene	0.0081	25	43	413	379	226	200	65
CAAACCATCC	KRT18, Keratin 18	0.0095	9	9	439	1235	154	143	133
GTGTGGGGGG	Junction plakoglobin	0.0096	6	3	29	64	50	56	61
TGCCCTCAGG	LCN2, Lipocalin 2 (oncogene 24p3)	0.0106	16	6	80	196	276	339	4
GCTGTTGCGC	-	0.0108	3	3	35	30	82	126	133
AAGAAGATAG	ribosomal protein L23a	0.0116	16	9	77	108	85	65	24
GAAAAAAAAA	SMAD, mothers against DPP homolog 3 (Drosophila)	0.0118	6	0	74	47	40	56	44
ACCTGTATCC	IFITM3, interferon induced transmembrane protein 3 (1-8U)	0.0123	13	3	26	81	64	82	53
CAACTTAGTT	myosin regulatory light chain MRLC2	0.0128	6	6	51	61	53	48	16
Down-regulated in pancreatic cancer
GACGACACGA	ribosomal protein S28	0.0001	428	388	109	122	90	117	154
GGACCACTGA	ribosomal protein L3	0.0002	310	270	102	105	101	104	61
GATCTCTTGG	S100 calcium binding protein A2	0.0002	188	174	3	10	8	4	0
AGCAGGAGCA	S100 calcium binding protein A16	0.0005	144	152	26	41	45	26	16
AGCTGTCCCC	capping protein (actin filament) muscle Z-line, beta	0.0005	219	254	13	3	3	4	0
GACTGCGCGT	tumor necrosis factor receptor superfamily, member 12A	0.0007	103	93	10	10	24	22	16
GTGGTGTGTG	congenital dyserythropoietic anemia, type I	0.0011	59	87	10	10	8	13	8
TAGGCATTCA	-	0.0012	119	115	0	0	0	0	0
TGAGTGGTCA	microtubule-associated protein 1 light chain 3 beta	0.0017	66	53	0	7	5	13	8
GGCGGCTGCA	excision repair cross- complementing rodent repair deficiency, group 1	0.0017	66	53	6	7	3	4	0
AAGTTTGCCT	glutaredoxin (thioltransferase)	0.0022	66	62	0	3	3	0	4
AGCTCTCCCT	Ribosomal protein L17	0.0023	335	357	77	145	82	143	125
CCGAAGTCGA	transcriptional regulating factor 1	0.0024	53	56	0	7	5	0	0
GCTGCTGCGC	-	0.0024	228	320	0	0	0	0	4
TTGGGAGCAG	isoleucine-tRNA synthetase	0.0031	72	43	10	10	19	4	8
TAAGGAGCTG	Ribosomal protein S26	0.0031	344	329	138	85	96	43	101
AACAGAAGCA	hypothetical protein FLJ25692	0.0031	75	59	13	24	24	9	16
CCTCCACCTA	peroxiredoxin 2	0.0031	56	43	16	10	3	9	4
TGTGAGTCAC	-	0.0038	31	62	0	0	0	0	0
TCAGGGATCT	-	0.0038	41	53	0	0	0	0	0

Note: tag counts have been converted to tags per 100,000 for comparison purposes. The p values listed are from the log-t test.

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ISSN: 1471-2105

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