Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)

Table 2 EBNA1 binding sites close to RefSeq genes

Chr	Start	End	Motif	RefSeq gene hit		Dist. to hit
chr1	52074635	52074636	Motif 5	NR_031580	MIR761	500
chr1	91738595	91738596	Motif 3	NM_001134419	CDC7	500
chr1	91739305	91739306	Motif 5	NM_001134420	CDC7	500
chr1	154170655	154170656		NM_014949	KIAA0907	500
chr10	61338790	61338791	Motif 2	NM_005436	CCDC6	3000
chr11	6421695	6421696		NM_000613	HPX	4000
chr12	67007430	67007431		NM_017440	MDM1	5000
chr12	108693660	108693661	Motif 2	NR_026661	MGC14436	4000
chr13	35769560	35769561	Motif 2	NM_001144985	C13orf38	500
chr13	35769000	35769001		NM_001144985	C13orf38	2000
chr14	50358425	50358426	Motif 5	NM_016350	NIN	3000
chr14	23969975	23969976	Motif 4.Motif 5	NM_015299	KHNYN	2000
chr14	104287630	104287631	Motif 5	NM_021709	SIVA1	4000
chr15	26999285	26999286		NM_001130414	APBA2	3000
chr16	3222305	3222306		NM_001145447	ZNF200	4000
chr16	3221595	3221596		NM_001145447	ZNF200	4000
chr17	71770850	71770851	Motif 2	NM_182565	FAM100B	4000
chr17	1335740	1335741	Motif 4	NM_001080950	MYO1C	500
chr17	58917775	58917776	Motif 2.Motif 5	NM_152830	ACE	3000
chr17	64015725	64015726		NM_212471	PRKAR1A	4000
chr2	190751405	190751406	Motif 5	NM_001042519	C2orf88	4000
chr20	49008975	49008976	Motif 2	NM_014484	MOCS3	500
chr20	36872330	36872331	Motif 2.Motif 5	NM_015568	PPP1R16B	5000
chr22	26645510	26645511		NR_026962	LOC284900	500
chr3	75761660	75761661		NR_031714	MIR1324	2000
chr6	18376590	18376591		NM_001134709	DEK	4000
chr6	149683865	149683866	Motif 5	NM_015093	MAP3K7IP2	4000
chr6	39190140	39190141		NM_018322	C6orf64	2000
chrX	41428495	41428496	Motif 2	NM_001097579	GPR34	5000

Each hit peak in the ChIP-seq enrichment list was labeled with our consensus motifs that lay within 50 nts upstream or downstream of the peak site. This annotated dataset was then used to search for overlaps with a list of RefSeq genes downloaded from the UCSC table browser. This overlap search was done with a Python script from Priyankara Wickramasinghe (Wistar Institute). Genes whose TSS lie within a distance of 500, 1000, 2000, 3000, 4000, and 5000 nt from EBNA1 ChIP-seq peaks were subsequently annotated on to the annotated hit peak list. The Galaxy suite http://main.g2.bx.psu.edu/ was used to combine and organize the various data lists in each step.

ISSN: 1743-422X