Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries

BMC Genomics

Table 8 LongSAGE tags corresponding to genes not previously reported to decrease expression in response to androgen in LNCaP cells^{a, n}

	Tags/100,000^{d, t}
LongSAGE Tag Sequence	Vehicle	R1881	Fold^{c, d, j}Change	RefSeq/Ensembl Access. No.	HGNC Gene Symbol	Description^φ
GTCTAGAATCTGTACCC	29	8	-4	NM_006407	ARL6IP5*	ADP-ribosylation-like factor 6 interacting protein 5
TCAAGAGCCGAAGGAAT	12	ND^b	-10	NM_014165	C6orf66*	Chromosome 6 open reading frame 66
GTATTTGCAAAAATGCC	118	24	-4.9	NM_018584	CAMK2N1*	Calcium/calmodulin-dependent protein kinase II inhibitor 1
AAAAGAGAAAGCACTTT	30	5	-6	NM_018584	CAMK2N1*	Calcium/calmodulin-dependent protein kinase II inhibitor 1
TTATAACTGAATTTAGT	51	11	-4.6	NM_006835	CCNI*	Cyclin I^{i, h}
GCCAGGAGAAGGGACAG	34	7	-5	NP_775809	CNBD1	N/A^m
TGGTACTCATTTCAGGC	12	ND	-10	NM_015954	DERA*	2-deoxyribose-5-phosphate aldolase homolog
AATCATAATGGATTCTT	16	ND	-20	NM_024641	MANEA*	Mannosidase, endo-alpha
CTAAGACTTCACCAGCC	19	2	-10	ENSG00000210082	N/A ^q	Non-coding predicted mitochondrial rRN A gene^k
CATTTGGTATTTTCGTC	30	8	-4	NC_001807^P	N/A	Intergenic region of mitochondrial genome
GTATTTCAGTGTCTGTC	33	9	-4	NM_015469	NIPSNAP3A*	Nipsnap homolog 3A
GTGTGTGGTGCCCCCAG	23	5	-5	NM_024066	PRNPIP*	Prion protein interacting protein
GTGTTAACCAGCTAAAG	122	60	-2.0	NM_002948	RPL15	Ribosomal protein L15
GCACAAGAAGATTAAAA	58	25	-2.3	NR_002746	SNORD47	Small nucleolar RNA, C/D box 47 on chromosome 1
AAAAAGCAGATGACTTG	77	37	-2.1	NM_000454	SOD1*	Superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult))
GTTTGGTTATAAATTCT	26	3	-10	NM_148893	SVIP*	Hypothetical protein DKFZp313A2432, transcript variant 1
TATTAGAGAATGAAAAG	17	2	-9	NM_016485	WA1*	VPS20-associated 1 homologue

a Statistics according to the Audic and Claverie test statistic (p ≤ 0.001)
b ND, not detected
c ND tags were assigned a value of 1 when calculating fold change
d Appropriate significant figures are displayed
h Gene known to change expression in response to androgens, but in the opposite direction as reported here
i Gene known to change expression in response to androgens in cells other than prostate
j Negative fold change value indicates down-regulation by R1881
k Tag has a single base pair permutation, insertion, or deletion with respect to gene
m Tag maps to the strand opposite of the gene
n Ambiguously mapped tags and tags with a fold change less than 2-fold have been excluded from the table
p NC_001807 refers to the complete genome of mitochondria in humans
All mitochondrial genes in the RefSeq database are assigned the same accession number by NCBI q N/A = there is no HGNC approved gene symbol for this tag t Tag count per 100,000 = (observed tag count/total tags in the library) × 100,000
φ In cases where a tag mapped to >1 transcript variant of the same gene the RefSeq accession number for transcript variant 1 was displayed * Gene further characterized in this paper

ISSN: 1471-2164