This track shows an estimate of the binding activity of 24
transcription factors in the D. melanogaster embryo.
Chromatin immunoprecipitation and whole-genome tiling arrays
(ChIP/chip) were used (see Li, MacArthur et al.)
to map the genomic regions bound by
22 sequence specific transcription factors
and two general transcription factors: TFIIB and the transcriptionally
active phosphorylated form of RNA polymerase II.
The sequence specific factors (except for
Zeste), described in the table below, fall into three
regulatory classes: anterior-posterior (A-P) early, A-P pair rule, and
dorsal-ventral (D-V).
Data for all proteins except Zeste are for stage 4-5 blastoderm
embryos. Data for Zeste are for stage 11 embryos.
Enrichment factors (1 = no enrichment) are shown in separate subtracks
for 36 antibodies at false discovery rates (FDR) of 1% and 25%.
By default, values are displayed in grayscale ("dense" mode)
instead of graphing ("full" mode), and only 24 of the 72
subtracks are shown: only those with FDR of 1% and only one antibody
per factor (the antibody with the most bound regions at FDR of 1%).
To change the configuration, click on the blue or gray
button to the left of the track or click on the track title in the
controls below the image.
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 controls page, followed by a list of
subtracks. To show only selected subtracks, uncheck the boxes next to
the tracks that you wish to hide.
For more information about the graphical configuration options, click the
Graph
configuration help link.
Subtracks are colored according to regulatory class:
green for A-P early,
orange for A-P pair rule,
blue for D-V,
brown for stage 11 zeste, and
red for general transcription factors.
Methods
Where practicable two antibody preparations that were independently
purified against nonoverlapping epitopes were used.
For each purified antibody, two independent replicates of three
different sample types were analyzed on separate arrays:
"Factor immunoprecipitates (IPs)" obtained by
immunoprecipitation using a factor-specific antibody
"immunoglobulin G (IgG) control IPs" obtained by
immunoprecipitation using a normal IgG antibody
"input DNA" obtained from the chromatin prior to
immunoprecipitation
for a total of six arrays per antibody.
Mean hybridization intensities for transcription factor IP replicates and
IgG control IP replicates were divided by the mean probe intensity
in the input DNA samples to produce oligonucleotide ratio values.
The logarithms of the oligonucleotide ratios were averaged in windows of
675 bp centered around each probe (after discarding the highest and lowest
values, to produce a "trimmed mean") to produce window scores.
Bound regions were identified by comparing window scores to expected score
distributions computed from a symmetric null distribution.
The symmetric null method assumes that the background window
score distribution is symmetric about its mean, and estimates the
distribution from values less than the observed mode.
This estimated null distribution was used to assign p-values to each
window score, and these were corrected for multiple testing to control
the FDR.
A separate FDR estimation method that uses
the IgG control data to estimate the null distribution defines a
similar number of bound regions (not shown here, see Li
et al., 2008).