Schema for modENCODE CAGE Tag Clusters - modENCODE CAGE Tag Clusters for Different Developmental Stages
  Database: dm6    Primary Table: modE_BG3_5hr_tagClusters    Row Count: 10,498   Data last updated: 2022-10-21
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 66543int(10) unsigned range
chromEnd 66547int(10) unsigned range
name .varchar(255) values
score 0int(10) unsigned range
strand +char(1) values
thickStart 66546int(10) unsigned range
thickEnd 66547int(10) unsigned range
reserved 0int(10) unsigned range
blockCount 3int(10) unsigned range
blockSizes 1,1,1longblob  
chromStarts 0,3,3longblob  

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr2L6654366547.0+6654666547031,1,10,3,3
585chr2L6704267044.0+6704367044031,2,10,0,1
585chr2L7259972617.0+7259972600031,4,10,0,17
585chr2L7342673441.0+7344073441031,15,10,0,14
585chr2L7352073523.0+7352273523031,3,10,0,2
585chr2L7410474115.0+7410474105031,11,10,0,10
585chr2L8737687382.0-8738187382031,6,10,0,5
585chr2L9472094770.0+9474194742031,18,10,14,49
585chr2L102381102436.0+102391102392031,35,10,4,54
585chr2L106692106733.0-106728106729031,32,10,5,40

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

modENCODE CAGE Tag Clusters (tss_modECAGE_tagClusters) Track Description
 

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.