PMC

(A) Array-CGH profile of chromosome 3p displaying a large 60.5 Mb terminal deletion in SK-N-AS. (B) Detailed view of the hemizygously deleted let-7 g/miR135a-1 locus. The upper two panels display the MYCN ChIP-chip raw log₂ ratios and identified peaks for both MYCN antibodies (NCMII-100 and B84b). Red and orange peaks represent regions of enrichment with an FDR of <0.05 and 0.05–0.1, respectively. MeDIP results for SK-N-AS are displayed in the lower panels in blue, which include log₂ ratios of MeDIP/Input, Kolmogorov-Smirnov test p-values (−log₁₀) and the merged statistically significant peaks of hypermethylation across the region. The position of CpG islands and orientation of miRNAs are displayed in the two bottom panels.

(A) Percentage of MYCN binding sites around transcription start sites. X-axis displays the distance in base pairs from UCSC annotated transcriptional start sites. Y-axis represents the percentage frequency of positive MYCN binding sites identified in each neuroblastoma cell line. (B) Prevalence of E-box motifs within MYCN binding sites detected by ChIP-chip across all cell lines and both antibodies. Statistically significant bars are indicated with their respective p-values (C) Prevalence of E-box motifs within the MYCN binding sites detected by ChIP-chip in the MYCN-amplified state only. Statistically significant bars are indicated with their respective p-values. (D) Association of E-box frequency with raw fluorescent ratios in MYCN binding sites on the promoter array which were detected in the Kelly NB cell line. The number of E-boxes per kilobase (y-axis) is plotted against the raw array fluorescent ratio intensities.

(A) Identification of MYCN binding upstream of NME2. The scale across the top of the panel indicates the base pair position on chromosome 17. Fluorescent intensity of probes from experiments using 2 independent MYCN antibodies around the NME2 promoter are expressed as log₂ ratios (green bars) and high confidence MYCN peaks (red bars) as identified by the NimbleScan peak finding algorithm. Position of the NME2 transcript and the region tiled on the array are indicated by the bottom two panels. (B) Total number of MYCN peaks identified across neuroblastoma cell lines. Venn diagrams (i–v) display the number of MYCN peaks which is shared and unique to each cell line. Statistical significance of overlap for all comparisons was determined to be statistically significant (P<0.001) by Fisher's Exact Test.