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. Clustered sites are shown in separate subtracks for each antibody:
Data for all biological replicates can be downloaded from Affymetrix in wiggle, cel, and soft formats.
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.
Three independent biological replicates were generated and hybridized to duplicate arrays (two technical replicates). Reproducible enriched regions were generated from the signal, by first applying a cutoff of 0.693(ln(2)=0.693) to the signal estimate, a maxgap and minrun of 500 and 0 basepairs respectively, to each biological replicate. Since each region or site can comprise of more than a single probe, a median based on the distribution of log transformed P-values was computed per site for each of the respective replicates. These seed sites were then ranked individually within each of the replicates. If a site was absent in a replicate the maximum or worst rank of the distribution was assigned to it.
The following three values were computed for each site by combining data from all biological replicates:
A final signal estimate based filter was applied, where sites with median signal estimate of at least 0.693/(total number of individual replcates) were considered. This was to ensure that if a site was not detected consistently in all replicates but was detected at a significant signal level in a subset of the replicates its detection level would be weighted accordingly in the final selection of sites. The final sites were selected when all of the above three metrics were relatively low, where "low" corresponds to the top 25 percentile of the distribution.
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.
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.
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).