Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites

Vega, Vinsensius B; Lin, Chin-Yo; Lai, Koon Siew; Li Kong, Say; Xie, Min; Su, Xiaodi; Teh, Huey Fang; Thomsen, Jane S; Li Yeo, Ai; Sung, Wing Kin; Bourque, Guillaume; Liu, Edison T

doi:10.1186/gb-2006-7-9-r82

Table 2 Validation results on genomic loci containing ERE-like sequences identified by sequencing random ChIP fragment from an ER ChIP library

From: Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites

Nearest gene	Genomic location	Pattern	Validation
NBPF4	chr1:108,492,542-108,492,560	ttaGGTCAgctTGTCCcag	Binding
C1orf21	chr1:181,327,606-181,327,624	ctgGGTCAgcaTGACCttc	Binding
	chr11:64,942,548-64,942,566	ctgGGGCAtgcTCACCtca	Binding
SEC15L2	chr2:72,713,948-72,713,966	ggaGGTCTaggTGACCtcg	Binding
	chr3:132,571,914-132,571,932	aggGGTCAtggTGACAtta	Binding
SLC6A6	chr3:14,429,604-14,429,622	ctgGGTCActgTGTCCgga	Binding
SIAH2	chr3:151,957,126-151,957,144	acaGGTCAccaTGACCtgg	Binding
SNX24	chr5:122,216,372-122,216,390	cagGGTTAtctTAACCaac	Binding
PKIB	chr6:122,985,938-122,985,956	tttGGTCAtgtGGGCCtga	Binding
	chr6:23,720,183-23,720,201	tcgGGTCAtgcTGCCTggg	Binding
BTBD9	chr6:38,337,561-38,337,579	tggGGTCAtggTGACTcct	Binding
SHB	chr9:37,943,504-37,943,522	gcaGGTGGggcTGCCTcca	Binding
SLC38A1	chr12:44,881,783-44,881,801	cagAGTGAactTGACCtga	Binding
SLC38A1	chr12:44,881,800-44,881,818	gagGGTCAtccCAACCcca	Binding
	chr16:2,781,142-2,781,160	ccaGGTCGgctTGCCCtta	Binding
	chr16:743,678-743,696	atgGGTCActgTGACCcag	Binding
	chr17:46,382,536-46,382,554	cccGGACAcgaTGTCCccc	Binding
TEX14	chr17:54,072,183-54,072,201	cacGGTCAtggTGACCtga	Binding
	chr20:54,945,262-54,945,280	gggAGACAcccTGACCtaa	Binding
	chr2:222,089,422-222,089,440	cagGTTCAaaaTGACGggt	Nonbinding
STK10	chr5:171,535,283-171,535,301	tgtGGTCTctgTGCCCagg	Nonbinding
KIAA1191	chr5:175,712,328-175,712,346	agaGGCCAgtcTACCCtcc	Nonbinding
RASGEF1C	chr5:179,478,929-179,478,947	gtgGGCCGgccTGGCCtgt	Nonbinding
SORCS1	chr10:108,692,194-108,692,212	cacAGTCAtgcTGACCcca	Nonbinding
	chr14:38,648,346-38,648,364	attGGTCAgagTGACAgaa	Nonbinding
	chr14:79,636,926-79,636,944	accTGGCAcgcTGACCcat	Nonbinding
LOC57149	chr16:20,819,825-20,819,843	tggGGTCAcacAGGCCcgt	Nonbinding
	chr16:25,535,373-25,535,391	ttaGTTCAcctTAACCcct	Nonbinding
CEACAM6	chr19:46,954,305-46,954,323	cagGACCAgggAGACCtga	Nonbinding

Shown in bold and underlined are nucleotides that deviate from the consensus core ERE. ChIP, chromatin immunoprecipitation; ER, estrogen receptor; ERE, estrogen response element.

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ISSN: 1474-760X

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