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Table 2 EBNA1 binding sites close to RefSeq genes

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

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
  1. 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.