This track shows an estimate of RNA abundance (transcription)
over the first 24 hours of D. melanogaster development in
two hour increments, measured by a tiling array as described in
Manak et al. (2006) (see References).
Composite signals are shown in
separate subtracks for each of the twelve timepoints.
Display Conventions and Configuration
The subtracks within this composite annotation track
may be configured in a variety of ways to highlight different aspects of the
displayed data. The graphical configuration options for the subtracks
are shown at the top of the track description page, followed by a list of
subtracks. To show only selected subtracks, uncheck the boxes next to
the tracks that you wish to hide.
For more information about the graphical configuration options, click the
configuration help link.
Color differences among the subtracks are arbitrary. They provide a
visual cue for distinguishing between the different timepoints.
The data were processed into signal and transfrags as described in
Cheng et al. (2005) and Kampa et al. (2004).
The data from replicate arrays were quantile-normalized and all arrays
were scaled to a median array intensity of 25. Within a sliding 101
bp window centered on each probe, an estimate of RNA abundance
(signal) was found by calculating the median of all pairwise average
PM-MM values, where PM is a perfect match and MM is a mismatch. This data
set was originally created for dm2(BDGP R4) and then lifted over to dm3(BDGP R5).
Samples were hybridized
to duplicate arrays (three technical replicates). Transcribed regions
were generated from the composite signal track by merging genomic positions
to which probes are mapped. This merging was based on a 5% false
positive rate cutoff in negative bacterial controls, a maximum
gap (MaxGap) of 50 base-pairs and minimum run (MinRun) of 90 base-pairs (see
the Affy TransFrags track for the merged regions).
These data were generated and analyzed by the Tom Gingeras group at
Please see the
Affymetrix Transcriptome site for a project overview and
additional references to Affymetrix tiling array publications.
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.
Science. 2005 May 20;308(5725):1149-54.
Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov
S, Helt G et al.
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and
Genome Res. 2004 Mar;14(3):331-42.
PMID: 14993201; PMC: PMC353210
Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, Long J, Cheng J, Bell I, Ghosh S, Piccolboni
A et al.
Biological function of unannotated transcription during the early development of Drosophila
Nat Genet. 2006 Oct;38(10):1151-8.