## Description

This track displays transcriptome data from tiling GeneChips produced by Affymetrix. For the complete non-repetitive portion of the human genome, more than 256 million probe pairs were tiled every 5 bp in non-repeat-masked areas and hybridized to cytosolic polyA+ long RNA (>200 nucleotides) from 8 different cell lines. Note that the female cell lines HeLa, SK-N-AS, and U87MG do not contain data for chrY. For the HeLa and HepG2 cell types, samples were also produced for nuclear RNA in addition to cytosolic polyA+ RNA. For experimental details and results, see Kapranov et al. in the References section below.

This track shows the coordinates of transcribed fragments (transfrags) representing long RNAs. A separate track -- "Affy Tx lRNA Sig" -- contains signals (PM-MM values) for each probe pair plotted against its genomic coordinates (see Kapranov et al. in the References section below).

## Display Conventions and Configuration

This annotation follows the display conventions for composite tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. For more information about the graphical configuration options, click the Graph configuration help link. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide.

## Methods

For each data point, probes within 30 bp on either side were used to improve the estimate of expression level for a particular probe. This helped to smooth the data and produce a more robust estimate of the transcription level at a particular genomic location. The following analysis steps were used:

1. Replicate arrays were quantile-normalized and the median intensity (using both PM and MM intensities) of each array was scaled to a target value of 50.
2. The expression level was estimated for each mapped probe position by collecting all the probe pairs that fell within a window of ± 30 bp, calculating all non-redundant pairwise averages of PM - MM values of all probe pairs in the window, and taking the median of all resulting pairwise averages.
3. The resulting signal value is the Hodges-Lehmann estimator associated with the Wilcoxon signed-rank statistic of the PM - MM values that lie within ± 30 bp of the sliding window centered at every genomic coordinate. These data are displayed in the track "Affy Tx lRNA Sig".
4. Transfrags were determined by connecting adjacent positive probes with a maximum allowable gap of 11 nucleotides and a minimum run of 49 nucleotides (at least 11 probes with at most one negative probe between two positive probes). Transfrags were discarded if they overlapped pseudogenes or harbored low-complexity or repetitive sequences.

## Credits

Data generation and analysis were performed by the transcriptome group at Affymetrix with assistance from colleagues at the University of Leipzig, Fraunhofer Institute, and University of Vienna: P. Kapranov, J. Cheng, S. Dike, D.A. Nix, R. Duttagupta, A.T. Willingham, P.F. Stadler, J. Hertel, J. Hackermüller, I.L. Hofacker, I. Bell, E. Cheung, J. Drenkow, E. Dumais, S. Patel, G. Helt, M. Ganesh, S. Ghosh, A. Piccolboni, V. Sementchenko, H. Tammana, T.R. Gingeras.

Questions or comments about this annotation? Email genome@soe.ucsc.edu.

## References

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007 Jun 8;316(5830):1484-8.