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 ID | Relative Expression | Color |
|---|
| 0_0 | Higher expression levels in the exosome-depleted sample than control | |
| 1_0 | Similar expression levels in the exosome-depleted and control samples | |
| 2_0 | Lower 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.
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