## Overview

This super-track combines related tracks of the ENCODE Extension data generated by Affymetrix. There are two member tracks:

- Affymetrix ENCODE Extension Transcription Sites: the transcribed fragments (transfrags) based on the signal.
- Affymetrix ENCODE Extension Transcription Signal: RNA abundance signal.

## 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 the University of Geneva.

## References

Please see the Affymetrix Transcriptome site for a project overview and additional references to Affymetrix tiling array publications.

Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 Jan 22;19(2):185-93.

Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004 Feb 20;116(4):499-509.

Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SP, Gingeras TR. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002 May 3;296(5569):916-9.