Schema for Exosome RNAi CAGE Tag Clusters - Exosome RNAi Knockdown CAGE Tag Clusters
  Database: dm6    Primary Table: GSE109588_CAGE_consensus    Row Count: 5,005   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 72599int(10) unsigned range
chromEnd 72673int(10) unsigned range
name 1_0varchar(255) values
score 0int(10) unsigned range
strand +char(1) values
thickStart 72599int(10) unsigned range
thickEnd 72673int(10) unsigned range
itemRgb 1710618int(10) unsigned range

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
585chr2L72599726731_00+725997267326,26,26
585chr2L87376873822_00-8737687382178,24,43
585chr2L1023811024200_00+10238110242033,102,172
585chr2L1067181067290_00-10671810672933,102,172
585chr2L1079251079691_00+10792510796926,26,26
585chr2L1081281081460_00+10812810814633,102,172
585chr2L1204741207620_00-12047412076233,102,172
585chr2L1210781210792_00+121078121079178,24,43
585chr2L1217451217900_00-12174512179033,102,172
585chr2L1292381292430_00-12923812924333,102,172

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

Exosome RNAi CAGE Tag Clusters (GSE109588_CAGEr_tagClusters) Track Description
 

Description

These tracks show the consensus clusters and the interquantile widths of the promoters based on CAGE data for exosome-depleted and control samples from D. melanogaster S2 cells. The CAGE datasets were obtained from the NCBI Sequence Read Archive database under the accession number SRP131270.

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(500, 50000), alpha = 1.07, 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

The self-organizing maps (SOM) consensus clusters were determined by the consensusClusters and getExpressionProfiles functions in CAGEr using the following parameters:

what = "consensusClusters", tpmThreshold = 10, nrPassThreshold = 1, method = "som", xDim = 3, yDim = 1

Display Conventions

For the tag clusters, 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.

For the consensus clusters, the color of the feature corresponds to the relative expression levels of the exosome-depleted and control samples:

Cluster IDRelative ExpressionColor
0_0Higher expression levels in the exosome-depleted sample than control
1_0Similar expression levels in the exosome-depleted and control samples
2_0Lower expression levels in the exosome-depleted sample than control

References

Rennie S, Dalby M, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T, Andersson R. Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. Nucleic Acids Res. 2018 Jun 20;46(11):5455-5469.

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.