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:
-
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.
-
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.
-
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".
-
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.
|
|