## Description

This track shows regions that co-precipitate with antibodies against each of 4 factors in all ENCODE regions, in retinoic-acid stimulated HL-60 (leukemia) cells harvested after 0, 2, 8, and 32 hours, and in a fifth factor tested in ME-180 cervical carcinoma cells. Median of the transformed P-value (-10 log[10] P) across processed replicate data is displayed as separate subtracks for each antibody:

- H4Kac4 (HisH4) - Histone H4 tetra-acetylated lysine
- H3K9K14ac2 (H3K9K14D) - Histone H3 K9 K14 Di-Acetylated
- Pol2 - RNA Polymerase II (8WG16 ab against pre-initiation complex form)
- p63_ActD - p63, in actinomycin-D treated ME-180 cells
- p63_mActD - p63 in untreated ME-180 cells

Retinoic acid-stimulated HL-60 cells and ME-180 cells (actinomycin-D treated or untreated) were harvested and whole cell extracts (control) were made. An antibody was used to immunoprecipitate bound chromatin fragments (treatment). DNA was purified from these samples and hybridized to Affymetrix ENCODE oligonucleotide tiling arrays, which have 25-mer probes tiled every 22 bp on average in the non-repetitive ENCODE regions.

Only the median of the transformed P-value (-10 log[10] P) is displayed; data for all biological replicates can be downloaded from Affymetrix in wiggle, cel, and soft formats.

## Display Conventions and Configuration

The subtracks within this composite annotation track may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options for the subtracks are shown at the top of the track description page, followed by a list of subtracks. For more information about the graphical configuration options, click the Graph configuration help link.

Color differences among the subtracks are arbitrary. They provide a visual cue for finding the same antibody in different timepoint tracks.

## Methods

The data from replicate arrays were quantile-normalized (Bolstad et al., 2003) and all arrays were scaled to a median array intensity of 22. Within a sliding 1001 bp window centered on each probe, a signal estimator S = ln[max(PM - MM, 1)] (where PM is perfect match and MM is mismatch) was computed for each biological replicate treatment- and all replicate control-probe pairs. An estimate of the significance of the enrichment of treatment signal for each replicate over control signal in each window was given by the P-value computed using the Wilcoxon Rank Sum test over each biological replicate treatment and all control signal estimates in that window. The median of the transformed P-value (-10 log[10] P) across processed replicate data is displayed.

## Verification

Using the P-values from the biological replicates, all pairwise rank correlation coefficients were computed among biological replicates. Data sets showing both consistent pairwise correlation coefficients and at least weak positive correlation across all pairs were considered reproducible.

## Credits

These data were generated and analyzed by the Gingeras/Struhl collaboration with the Tom Gingeras group at Affymetrix and Kevin Struhl's group at Harvard Medical School.

## References

Please see the Affymetrix Transcriptome site for a project overview and additional references to Affymetrix tiling array publications.

Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19(2), 185-193 (2003).

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116(4), 499-509 (2004).

Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell. 24(4), 593-602 (2006).