Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation

Sievertzon, Maria; Wirta, Valtteri; Mercer, Alex; Frisén, Jonas; Lundeberg, Joakim

doi:10.1186/1471-2202-6-55

Table 1 Top differentially expressed genes in the overlap between all treatments.

From: Epidermal growth factor (EGF) withdrawal masks gene expression differences in the study of pituitary adenylate cyclase-activating polypeptide (PACAP) activation of primary neural stem cell proliferation

Unigene ID	Gene ID	GeneName	Avg M	Stdev M	Avg B	Stdev B
Mm.305535	69719	Carbamoyl-phosphate synthetase 2	4.53	0.26	53.33	4.34
Mm.1239	14580	Glial fibrillary acidic protein	4.47	0.39	69.36	3.97
Mm.252063	17196	Myelin basic protein	3.84	0.57	47.80	7.00
Mm.200608	12759	Clusterin	3.72	0.54	60.76	7.92
Mm.240850	76960	Breast carcinoma amplified sequence 1	3.72	0.17	46.89	1.30
Mm.291129	70877	RIKEN cDNA 4921517J23 gene	3.68	0.44	49.64	6.06
Mm.1268	18823	Proteolipid protein (myelin) 1	3.64	0.49	51.72	4.02
Mm.305152	11816	Apolipoprotein E	3.62	0.46	45.79	11.39
Mm.334994	53867	Procollagen. type V. alpha 3	3.61	0.45	49.05	8.48
Mm.272443	64383	Sirtuin 2	3.33	0.34	72.98	3.98
Mm.7420	22153	Tubulin. beta 4	3.13	0.38	53.65	4.65
Mm.39053	71770	Adaptor-related protein complex 2. beta 1 subunit	2.92	0.61	32.53	10.40
Mm.228362	NA	Transcribed locus	2.69	0.15	39.82	3.13
Mm.358573	11858	Ras homolog gene family. member N	2.68	0.39	52.12	7.88
Mm.276739	20665	SRY-box containing gene 10	2.65	0.34	33.25	1.34
Mm.241355	17136	Myelin-associated glycoprotein	2.57	0.59	32.28	6.80
Mm.278672	14810	Glutamate receptor. ionotropic. NMDA1 (zeta 1)	2.56	0.52	35.15	7.11
Mm.260601	242521	Kelch-like 9 (Drosophila)	2.54	0.41	44.19	9.26
Mm.192991	17748	Metallothionein 1	2.47	0.54	21.61	5.08
Mm.37199	14862	Glutathione S-transferase. mu 1	2.44	0.16	38.61	2.15
Mm.41580	69908	RAB3B. member RAS oncogene family	-3.55	0.31	47.83	4.75
Mm.290563	12615	Centromere autoantigen A	-3.14	0.16	49.02	3.58
NA	NA	GenBank ID: CX204578	-3.09	0.34	34.48	2.55
NA	NA	GenBank ID: CX207566	-2.99	0.27	51.46	6.04
Mm.273049	12443	Cyclin D1	-2.89	0.33	44.78	3.46
Mm.289747	107995	Cell division cycle 20 homolog (S. cerevisiae)	-2.68	0.15	55.41	5.67
Mm.285723	14793	Cell division cycle associated 3	-2.65	0.08	42.97	0.95
Mm.24337	52033	PDZ binding kinase	-2.58	0.12	40.31	2.70
Mm.29254	16009	Insulin-like growth factor binding protein 3	-2.49	0.29	41.37	3.97
Mm.233799	16010	Insulin-like growth factor binding protein 4	-2.46	0.31	23.86	5.98
Mm.16525	18817	Polo-like kinase 1 (Drosophila)	-2.43	0.12	26.12	1.92
Mm.28038	52276	Cell division cycle associated 8	-2.39	0.12	30.79	5.44
Mm.4857	12323	Calcium/calmodulin-dependent protein kinase II. beta	-2.38	0.49	42.14	5.06
Mm.335368	NA	CDNA. clone:Y2G0133B03:ENSEMBL	-2.35	0.25	50.92	4.35
NA	NA	GenBank ID: CX206925	-2.32	0.13	28.39	1.66
Mm.271711	21346	Transgelin 2	-2.25	0.12	38.33	1.70
Mm.4237	21973	Topoisomerase (DNA) II alpha	-2.14	0.12	46.22	2.01
Mm.1408	11535	Adrenomedullin	-2.07	0.17	26.68	5.70
Mm.37802	69544	WD repeat domain 5B	-2.03	0.10	59.04	2.30
Mm.35389	13063	Cytochrome c. somatic	-2.02	0.12	51.69	2.15

The top of the table shows genes that are up-regulated in the treated (EGF withdrawn) samples, compared to the undifferentiated neurospheres (NS) (positive M-values). The lower half of the table shows genes that are up-regulated in the NS sample (negative M-values). Average M- and B-values for all comparisons (NS vs. PACAP, NS vs. Prol Cont and NS vs. Diff Cont) are shown, together with their standard deviations. All genes have a p-value < 0.0001, calculated by empirical Bayes moderated t-test and a Holm adjustment for multiple testing.

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ISSN: 1471-2202

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