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. 2009 Jun 2;37(14):4587–4602. doi: 10.1093/nar/gkp425

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© 2009 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — (A and B) Binding site enrichment analysis. The program MOTIFCLASS was employed to identify binding sites significantly over-represented in the promoters of genes that respond to hypoxia in B cells. (A) Totally 770 promoters of genes that responded to hypoxia in which a detectable HIF-1-binding site was identified. HIF-1 PWMs were identified as the most enriched. (B) Totally 1456 promoters of genes that responded to hypoxia but do not contain a detectable HIF-1-binding site. No HIF-1 PWM was identified in the top 20 matrices. Sn, sensitivity; Sp, specificity; Error, classification error rate; Pval, P-value. (C) Correlation between the number of HIF-target genes and the number of cells in which they responded to hypoxia. Only 31% of the genes that responded to hypoxia in one of six cells was predicted as a HIF-target gene, compared to 71% of the genes that responded to hypoxia in six of six cell lines.