Description
This track shows an estimate of RNA abundance (transcription) for chromosomes 21 
and 22 for 5 cell lines and 11 tissues. The 5 cell lines used were: GM06990, 
HepG2, K562, HeLaS3 and Tert-BJ; the 11 tissues used were: cerebellum, brain 
frontal lobe, hippocampus, hypothalamus, fetal spleen, fetal kidney, fetal thymus, 
ovary, placenta, prostate and testis. Purified cytosolic polyA+ RNA from GM06990, 
HepG2 and Tert-BJ cell lines, as well as purified polyA+ RNA from whole cell 
extracts of the remaining cell lines and tissues, were hybridized to Affymetrix 
Chromosome 21_22_v2 oligonucleotide tiling arrays, which have 25-mer probes 
spaced on average every 17 bp (center-center of each 25mer) in the non-repetitive 
regions of human chromosomes 21 and 22. Composite signals are shown in separate 
subtracks for each cell and tissue types. 
Data for all biological replicates can be 
downloaded from Affymetrix in wig, BED, and cel formats.
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 Graph configuration help
link.
  
Methods
The data from replicate arrays were quantile-normalized (Bolstad et al., 
2003) and all arrays were scaled to a median array intensity of 330. Using two 
different approaches: i) no sliding window ii) sliding 51-bp window centered on 
each probe, an estimate of RNA abundance (signal) was computed by calculating 
the median of all pairwise average PM-MM values, where PM is a perfect match 
and MM is a mismatch. Both Kapranov et al. (2002) and Cawley 
et al.  (2004) are good references for the experimental methods.  The 
latter also describes the analytical methods.
Verification
Single biological replicates were generated and hybridized to duplicate arrays 
(two 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 25 basepairs and minimum run (MinRun) of 
25 basepairs (see the Affy TransFrags track for the merged regions). 
 
Credits
These data were generated and analyzed by the collaboration of the following 
groups: the Tom Gingeras group at Affymetrix, Roderic Guigo group at Centre 
de Regulacio Genomica, Alexandre Reymond group at the University of Lausanne 
and Stylianos Antonarakis group at University of Geneva. 
 
References
Please see the Affymetrix 
Transcriptome site for a project overview and additional references to 
Affymetrix tiling array publications.
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. A
comparison of normalization methods for high density oligonucleotide
array data based on variance and bias. Bioinformatics 19(2),
185-193 (2003).
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A.,
Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams,
A. J., et al. Unbiased mapping of transcription factor binding sites along human 
chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 
116(4), 499-509 (2004).
Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg,
R. L., Fodor, S. P., and Gingeras, T. R. Large-scale transcriptional activity in chromosomes 21 and 
22. Science 296(5569), 916-919 (2002).