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Figure 3 | BMC Bioinformatics

Figure 3

From: Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas

Figure 3

Confirmation of PBM-mapping predicted sites by EMSA and ChIP Analysis. (A) EMSA analysis of selected predicted sites. Probes spanning approximately 50-60 bp surrounding the predicted site were incubated with in vitro synthesized Nkx2.2. The Nkx2.2 consensus probe and the consensus probe with the core sequence deleted were used as positive and negative controls, respectively. (B) Confirmation of in vivo promoter occupancy at predicted sites by ChIP. βTC6 cells were used for chromatin input and the Nkx2.2 mouse monoclonal antibody was used for precipitations. Enrichment is shown as fold change over IgG. All predicted sites were significantly increased over the IgG control (P < 0.05). The housekeeping gene GapdH was used as a negative control and was not significantly enriched.

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BMC Bioinformatics

ISSN: 1471-2105

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