Figure 1.
Distribution of Sequence Attributes
Distribution of sequence attributes used as input for the Bayesian classification.
(A) Distribution of distances to transcription start site.
(B) Distribution of distances to nearest CpG islands.
(C) Distribution of distances to nearest hypomethylation region.
(D) Distribution of PhastCons scores from the UCSC genome database.
(E) Distribution of distances to nearest chromatin acetylation island.
Sequence distance is shown in base pairs. All of the distances were natural log transformed.
Figure 2.
Topology of the Bayesian network classifier for high-occupancy MYC binding obtained by training. The detailed parameters for the model are provided in Figure S2.
Table 1.
Comparison of Predicted MYC Binding Loci with Published Experimental Datasets
Table 2.
Performance on MYC High-Occupancy Sites Prediction
Table 3.
Performance on MYC Binding Gene Predictions
Table 4.
Prediction of CREB Occupancy in Genes Manually Assayed by ChIP
Table 5.
Prediction of CREB Occupancy in Promoters Assayed by ChIP–chip
Figure 3.
c-MYC Expression Level in Both Tissues
The RMA normalized signal intensity of c-MYC probe sets in B cells (upper) and prostates (lower). Green, c-MYC probe set “1827_s_at”; red, c-MYC probe set “1973_s_at”; blue, c-MYC probe set “37724_at.”
Figure 4.
Distribution of c-MYC Co-Expression Coefficients in B cells and in Prostate Cancers
Distribution of correlation coefficients for c-MYC with genes in B cells (A) and prostate cancers (B). The predicted genes in Figure 4 refer to the high-occupancy MYC binding and MYC target gene predictions.
Figure 5.
Expression of Known c-MYC Targets in Both Tissues
Pearson's correlation coefficient of MYC target genes in B cells and prostate cancers. The MYC target genes were from MYC Target Gene Database.
Table 6.
Summary of MYC Targets Prediction from Different Microarray Datasets
Figure 6.
Overlaps of c-MYC Targets Genes
Venn diagrams for the overlap between the set of c-MYC target genes identified in the different experimental and theoretical studies.
Table 7.
Comparison of Different MYC Binding Datasets to Genes in MYC Target Database