modENCODE CAGE Tag Clusters Track Settings
 
modENCODE CAGE Tag Clusters for Different Developmental Stages   (All Expression and Regulation tracks)

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  StageGroup Embryo  Larva  WPP  Pupa  Adult  BG3  Kc167  S2 
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 Embryos, 0-2 hr  modENCODE CAGE Tag Clusters for 0-2 hr Embryos   Schema 
 
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 Embryos, 2-4 hr  modENCODE CAGE Tag Clusters for 2-4 hr Embryos   Schema 
 
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 Embryos, 4-6 hr  modENCODE CAGE Tag Clusters for 4-6 hr Embryos   Schema 
 
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 Embryos, 6-8 hr  modENCODE CAGE Tag Clusters for 6-8 hr Embryos   Schema 
 
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 Embryos, 8-10 hr  modENCODE CAGE Tag Clusters for 8-10 hr Embryos   Schema 
 
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 Embryos, 12-14 hr  modENCODE CAGE Tag Clusters for 12-14 hr Embryos   Schema 
 
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 Embryos, 16-18 hr  modENCODE CAGE Tag Clusters for 16-18 hr Embryos   Schema 
 
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 Embryos, 20-22 hr  modENCODE CAGE Tag Clusters for 20-22 hr Embryos   Schema 
 
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 L1  modENCODE CAGE Tag Clusters for L1 Stage Larvae   Schema 
 
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 L2  modENCODE CAGE Tag Clusters for L2 Stage Larvae   Schema 
 
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 L3, 12hr Post-Molt  modENCODE CAGE Tag Clusters for L3 Stage Larvae, 12 hr Post-Molt   Schema 
 
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 L3, Blue Gut  modENCODE CAGE Tag Clusters for L3 Stage Larvae, Light Blue Gut   Schema 
 
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 L3, CNS  modENCODE CAGE Tag Clusters for L3 Stage Larvae, CNS   Schema 
 
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 L3, Carcass  modENCODE CAGE Tag Clusters for L3 Stage Larvae, Carcass   Schema 
 
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 L3, Digestive System  modENCODE CAGE Tag Clusters for L3 Stage Larvae, Digestive System   Schema 
 
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 L3, Imaginal Discs  modENCODE CAGE Tag Clusters for L3 Stage Larvae, Imaginal Discs   Schema 
 
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 WPP, 2 days CNS  modENCODE CAGE Tag Clusters for WPP + 2 days, CNS   Schema 
 
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 WPP, 2 days Fat  modENCODE CAGE Tag Clusters for WPP + 2 days, Fat   Schema 
 
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 Pupae, 12 hrs after WPP  modENCODE CAGE Tag Clusters for Pupae, 12 hrs after WPP   Schema 
 
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 Pupae, 2 days after WPP  modENCODE CAGE Tag Clusters for Pupae, 2 days after WPP   Schema 
 
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 Adult Mated Female, 1 day Heads  modENCODE CAGE Tag Clusters for Adult Mated Female, 1 day Post-eclosion Heads   Schema 
 
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 Adult Mated Female, 4 days Ovaries  modENCODE CAGE Tag Clusters for Adult Mated Female, 4 days Post-eclosion Ovaries   Schema 
 
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 Adult Mated Female, 20 days Heads  modENCODE CAGE Tag Clusters for Adult Mated Female, 20 days Post-eclosion Heads   Schema 
 
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 Adult Mated Male, 1 day Heads  modENCODE CAGE Tag Clusters for Adult Mated Male, 1 day Post-eclosion Heads   Schema 
 
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 Adult Mated Male, 4 days Testes  modENCODE CAGE Tag Clusters for Adult Mated Male, 4 days Post-eclosion Testes   Schema 
 
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 Adult Mated Male, 4 days Glands  modENCODE CAGE Tag Clusters for Adult Mated Male, 4 days Post-eclosion Male Accessory Glands   Schema 
 
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 Adult Mated Male, 20 days Heads  modENCODE CAGE Tag Clusters for Adult Mated Male, 20 days Post-eclosion Heads   Schema 
 
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 Adult Virgin Female, 4 days Ovaries  modENCODE CAGE Tag Clusters for Adult Virgin Female, 4 days Post-eclosion Ovaries   Schema 
 
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 Mixed Adults, 4 days Carcass  modENCODE CAGE Tag Clusters for Adult Mixed Male and Female, 4 days Post-eclosion Carcass   Schema 
 
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 Mixed Adults, 4 days Digestive System  modENCODE CAGE Tag Clusters for Adult Mixed Male and Female, 4 days Post-eclosion Digestive System   Schema 
 
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 Mixed Adults, 20 days Digestive System  modENCODE CAGE Tag Clusters for Adult Mixed Male and Female, 20 days Post-eclosion Digestive System   Schema 
 
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 BG3, 0 hr Ecdysone  modENCODE CAGE Tag Clusters for BG3 Cells, 0 hr Ecdysone   Schema 
 
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 BG3, 5 hrs Ecdysone  modENCODE CAGE Tag Clusters for BG3 Cells, 5 hrs Ecdysone   Schema 
 
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 BG3, 24hrs Ecdysone  modENCODE CAGE Tag Clusters for BG3 Cells, 24 hrs Ecdysone   Schema 
 
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 Kc167, Cytoplasm  modENCODE CAGE Tag Clusters for Kc167 Cells, Cytoplasm RNA   Schema 
 
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 Kc167, Nuclear  modENCODE CAGE Tag Clusters for Kc167 Cells, Nuclear RNA   Schema 
 
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 S2  modENCODE CAGE Tag Clusters for S2 Cells, DRSC   Schema 
    

Description

These tracks show the interquantile widths of the promoters based on CAGE data for different developmental stages of D. melanogaster. The CAGE datasets were produced by the modENCODE project and were obtained from the NCBI Sequence Read Archive database under the accession number SRP001602.

Methods

Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. The alignment results were analyzed by CAGEr. The tag counts were normalized by the normalizeTagCount function in CAGEr with the following parameters:

method = "powerLaw", fitInRange = c(10, 1000), alpha = 1.05, T = 1*10^6

The promoter widths were determined by the cumulativeCTSSdistribution and quantilePositions functions in CAGEr using the following parameters:

clusters = "tagClusters", qLow = 0.1, qUp = 0.9

Display Conventions

The span of each feature corresponds to the promoter width. The thin box within each span corresponds to the interquantile width (qLow = 0.1 to qUp = 0.9) that captures 80% of the CAGE signal. The thicker box denotes the position within the promoter with the highest CAGE signal.

Credits

Hoskins RA, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb;21(2):182-92.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 2015 Apr 30;43(8):e51.