BDTNP ChIP/chip: Medea (med) antibody 2, stage 14 embryos, False Discovery Rate (FDR) 1% (bdtnpMed2S14Fdr1)
  Position: chr2L:826,001-851,000
Total Bases in view: 25,000
Statistics on: 95 items covering 95 bases (0.38% coverage)
Average item spans 1.00 bases.
Average value 1.63262 min 1.21928 max 2.38176 standard deviation 0.318456
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Data last updated: 2010-08-27 11:28:27

Description

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%.

Seq. Specific Factor SymbolDNA binding domainRegulatory Class
Bicoid bcdhomeodomainA-P early maternal
Caudal cadhomeodomainA-P early maternal
Giant gtb-zip domainA-P early gap
Hunchback hbC2H2 Zinc fingerA-P early gap
Knirps knireceptor Zinc fingerA-P early gap
Krüppel KrC2H2 Zinc fingerA-P early gap
Huckebein hkbC2H2 Zinc fingerA-P early terminal
Tailless tllreceptor Zinc fingerA-P early terminal
Dichaete DHMG/SOX classA-P early gap-like
Fushi tarazu ftzhomeodomainA-P pair rule
Hairy hbHLHA-P pair rule
Paired prdhomeodomain / paired domainA-P pair rule
Runt runrunt domainA-P pair rule
Sloppy paired 1 slp1forkhead domainA-P pair rule
Daughterless dabHLHD-V maternal
Dorsal dlNFkB/relD-V maternal
Mothers against dpp madSMAD-MH1D-V zygotic
Medea medSMAD-MH1D-V zygotic
Schnurri shnC2H2 Zinc fingerD-V zygotic
Snail snaC2H2 Zinc fingerD-V zygotic
Twist twibHLHD-V zygotic
Zeste zuniqueubiquitous

Display Conventions and Configuration

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).

Credits

Thanks to the Berkeley Drosophila Transcription Network Project's In Vivo DNA Binding collaboration, and Stewart MacArthur and Mark Biggin in particular, for these data.

References

Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008 Feb;6(2):e27. PMID: 18271625; PMC: PMC2235902

MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009;10(7):R80. PMID: 19627575; PMC: PMC2728534

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol. 2006 Oct;2(10):e130. PMID: 17040121; PMC: PMC1599766

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE et al. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011;12(5):R43. PMID: 21569360; PMC: PMC3219966