Description

This track displays transcriptome data from tiling GeneChips produced by Affymetrix. For the ten chromosomes 6, 7, 13, 14, 19, 20, 21, 22, X, and Y, more than 74 million probes were tiled every 5 bp in non-repeat-masked areas and hybridized to mRNA from 11 different cell lines (some cell lines were female and contain no data for chrY). For HepG2, some samples were depleted of polyA transcripts rather than enriched. For experimental details and results, see Cheng 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.

Each subtrack is colored blue in areas that are thought to be transcribed at a statistically significant level as described in the accompanying transfrags (transcribed fragments) track. Transfrags that have a significant blat hit elsewhere in the genome are displayed in a lighter shade of blue, and transfrags that overlap putative pseudogenes are colored an even lighter shade of blue. All other regions of the track are colored brown. While the raw data are based on perfect match minus mismatch (PM - MM) probe values and may contain negative values, the track has a minimum value of zero for visualization purposes.

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 method was 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 44.
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
   • 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.

Credits

Data generation and analysis was performed by the transcriptome group at Affymetrix: Bekiranov S, Brubaker S, Cheng J, Dike S, Drenkow J, Ghosh S, Gingeras T, Helt G, Kampa D, Kapranov P, Long J, Madhavan G, Manak J, Patel S, Piccolboni A, Sementchenko V, and Tammana H.

UCSC annotation performed by Chuck Sugnet.

References

Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science. 2005 May 20;308(5725):1149-54.