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

BMC Genomics

Table 6 LongSAGE tags corresponding to genes known to decrease expression in response to androgen in LNCaP cells^{a, n}

	Tags/100,000^{d, t}
LongSAGE Tag Sequence	Vehicle	R1881	Fold Change^{c, d, j}	RefSeq/Ensembl Access. No.	HGNC Gene Symbol	Description^φ
CAAAAGCTTATTCTTGT	29	3	-10	NM_016613	C4orf18	Chromosome 4 open reading frame 18, transcript variant 2
TCACACAGTGCCTGTCG	19	1	-20	NM_020311	CXCR7*	Chemokine orphan receptor 1
ACAAACCCCCACCCCAG	41	7	-6	NM_013330	NME7	Non-metastatic cells 7, protein expressed in, transcript variant 1, Nucleoside diphosphate kinase
AATCTCTCAATTATAGG	34	9	-4	NM_006183	NTS*	Neurotensin
ATCAACTGGAGGCTCAG	15	ND^b	-20	NM_005013	NUCB2	Nucleobindin 2
CCAAAATTAGGAAAAAC	15	1	-20	NM_002577	PAK2	p21 (CDKNlA)-activated kinase 2^k
TTACGTTTGGGAAAAAT	19	2	-9	NM_032971	PCDH11Y	Protocadherin 11 Y-linked, transcript variant a^k
TGACTTTGGTGCCGTTA	12	ND	-10	NM_003629	PIK3R3	Phosphoinositide-3-kinase, regulatory subunit 3 (p55, gamma)
AGCAAATATGTCAAGGG	47	16	-2.9	NM_182948	PRKACB*	Protein kinase, cAMP-dependent, catalytic, beta, transcript variant 1
GACTATTCCATATTAAA	27	1	-30	NM_018412	ST7*	Suppression of tumorigenicity 7, transcript variant A
GAGGGTTTTAAATGGAG	79	9	-9	NM_001077	UGT2B17	UDP glucuronosyltransferase 2 family, polypeptide B17

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
j Negative fold change value indicates down-regulation in response to R1881
k Tag has a single base pair permutation, insertion, or deletion with respect to gene
n Ambiguously mapped tags and tags with a fold change less than 2-fold have been excluded from table
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