modENCODE CAGE Tag Clusters Track Settings

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

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