BDTNP ChIP/chip Track Settings
 
Berkeley Drosophila Transcription Network Project Transcription Factor ChIP/chip   (All Expression and Regulation tracks)

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  Stage: Stage 4-5 Stage 9 Stage 10 Stage 11 Stage 14
 All Regulatory class Anterior-posterior early maternal  Anterior-posterior early gap  Anterior-posterior early terminal  Anterior-posterior early gap-like  Anterior-posterior pair rule  Dorsal-ventral maternal  Dorsal-ventral zygotic  Zeste stage 11  General Regulatory classAll 
Factor Factor
bicoid   bicoid
caudal   caudal
giant   giant
hunchback   hunchback
knirps   knirps
Kruppel   Kruppel
huckebein   huckebein
tailless   tailless
Dichaete   Dichaete
fushi tarazu   fushi tarazu
hairy   hairy
paired   paired
runt   runt
sloppy paired 1   sloppy paired 1
daughterless   daughterless
dorsal   dorsal
Mothers against dpp   Mothers against dpp
Medea   Medea
schnurri   schnurri
snail   snail
twist   twist
zeste   zeste
PolII   PolII
Transcription factor IIB   Transcription factor IIB
Factor Factor
 All Regulatory class Anterior-posterior early maternal  Anterior-posterior early gap  Anterior-posterior early terminal  Anterior-posterior early gap-like  Anterior-posterior pair rule  Dorsal-ventral maternal  Dorsal-ventral zygotic  Zeste stage 11  General Regulatory classAll 
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  Regulatory class↓1 Factor↓2 views↓3 Stage↓4   Track Name↓5  
 
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 Anterior-posterior early maternal  bicoid  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: bicoid (bcd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early maternal  caudal  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: caudal (cad) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early gap  giant  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: giant (gt) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early gap  hunchback  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: hunchback (hb) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early gap  hunchback  Best Antibody (FDR=1%)  Stage 9  BDTNP ChIP/chip: hunchback (hb) antibody 1, stage 9 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early gap  knirps  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: knirps (kni) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early gap  Kruppel  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: Kruppel (Kr) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early terminal  huckebein  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: huckebein (hkb) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early terminal  tailless  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: tailless (tll) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior early gap-like  Dichaete  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: Dichaete (D) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior pair rule  fushi tarazu  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: fushi tarazu (ftz) antibody 3, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior pair rule  hairy  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: hairy (h) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior pair rule  paired  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: paired (prd) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior pair rule  runt  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: runt (run) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Anterior-posterior pair rule  sloppy paired 1  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: sloppy paired 1 (slp1) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral maternal  daughterless  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: daughterless (da) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral maternal  dorsal  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: dorsal (dl) antibody 3, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral zygotic  Mothers against dpp  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: Mothers against dpp (mad) antibody 2, stage 4-5 embryos, False Disc. Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral zygotic  Medea  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: Medea (med) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral zygotic  Medea  Best Antibody (FDR=1%)  Stage 10  BDTNP ChIP/chip: Medea (med) antibody 2, stage 10 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral zygotic  Medea  Best Antibody (FDR=1%)  Stage 14  BDTNP ChIP/chip: Medea (med) antibody 2, stage 14 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral zygotic  schnurri  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: schnurri (shn) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral zygotic  snail  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: snail (sna) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Dorsal-ventral zygotic  twist  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: twist (twi) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 Zeste stage 11  zeste  Best Antibody (FDR=1%)  Stage 11  BDTNP ChIP/chip: zeste (z) antibody 2, stage 11 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 General  PolII  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: RNA Polymerase II (PolII) antibody, stage 4-5 embryos, False Discovery Rate (FDR) 1%   Schema 
 
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 General  Transcription factor IIB  Best Antibody (FDR=1%)  Stage 4-5  BDTNP ChIP/chip: Transc. factor IIB (TFIIB) antibody 1, stage 4-5 embryos, False Disc. Rate (FDR) 1%   Schema 
    

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