A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays

BMC Genomics

Table 2 Comparison of CREB HaloCHIP-chip and CREB ChIP-chip data.

HaloCHIP-chip:ChIP-chip compared	Number of Promoters	Percentage Overlap	Enrichment over Random
Top 1%	96/277	35%	44
Top 5%	616/1383	45%	10
Top 1%*	47/182	26%	5
Top 5%*	212/898	24%	5
HaloCHIP-chip:HaloCHIP-chip compared	Number of Promoters	Percentage Overlap	Enrichment over Random
Top 1%	140/277	51%	65
Top 5%	734/1383	53%	11
ChIP-chip:ChIP-chip compared	Number of Promoters	Percentage Overlap	Enrichment over Random
Top 1%	115/277	42%	53
Top 5%	477/1383	34%	7

The number of promoters found to overlap between the CREB HaloCHIP-chip and standard ChIP-chip experiments were determined for both the Top 1% and 5% of each respective list. Also shown is the calculation of the fold enrichment over what is expected for a randomized comparison. The first Top 1 and 5% overlap is between CREB HaloCHIP-chip and ChIP-chip data obtained from the same probes and arrays, therefore the number of promoters, 277 and 1383 respectively, used for comparison is the same between the two lists. The (*) indicates the comparison of the HaloCHIP-chip array data to previously published Top 1 and 5% CREB ChIP-chip data [29]. The Top 1 and 5% CREB ChIP-chip data correspond to 182 and 898 promoters respectively, and it was these which were used for the comparison to the Top 1 and 5% of the HaloCHIP-chip array data. Calculated in a similar fashion is the percentage overlap and enrichment over random between HaloCHIP-chip biological replicate sets or ChIP-chip biological replicate data sets.

ISSN: 1471-2164