This track shows expression of
target RNA binding proteins (RBPs)
as measured by RNA-binding protein immunoprecipitation-microarray profiling
(RIP-chip) using different
The RBP Assoc RNA view shows the genomic location of transcripts
associated with the array probes.
Data for this track was produced as part of the
Encyclopedia of DNA Elements (ENCODE) Project,
In eukaryotic organisms gene regulatory networks require an additional
level of coordination that links transcriptional and post-transcriptional
processes. Messenger RNAs have traditionally been viewed as passive
molecules in the pathway from transcription to translation. However,
it is now clear that RNA-binding proteins play a major role in
regulating multiple mRNAs in order to facilitate gene expression patterns.
These tracks show the associated mRNAs that co-precipitate with the
targeted RNA-binding proteins using RIP-Chip profiling.
Display Conventions and Configuration
This track is a multi-view composite track. For each view there
are multiple subtracks that display individually in the browser.
The subtracks within this track correspond to different antibodies/target
proteins tested in different cell lines.
This track is initially released with a single view:
Instructions for configuring multi-view tracks are
- RBP Assoc RNA
- The RBP Assoc RNA view shows the genomic extent of the transcripts
the Affymetrix Exon Array probes, shaded according to score.
RBP-mRNA complexes were purified from cells grown according to the approved
ENCODE cell culture protocols .
The associated messages were identified using Affymetrix
Human Exon 1.0 ST Arrays.
Measurements of expression at gene-level were extracted using
Affymetrix tools, and were further processed
to generate average fold-change and p-values for immunoprecipitation.
Enriched regions were scored in the range ~100 to ~1000, and interrogated
regions without significant signal were scored at 1.
The signal value contains the minimum log2 fold-change, the p-value
contains -log10 of the maximum p-value, and the q-value was
left at the default of -1.
For additional methods detail, see
Tenenbaum et al. 2002; Baroni et al. 2008; Penalva
et al. 2004, below.
Details of the RIP-chip analysis methods are available
These data were produced and analyzed by a collaboration between the
at the University at Albany-SUNY, Gen*NY*Sis Center For Excellence
in Cancer Genomics and the
Luiz Penalva group
at the Greehey Children's Cancer Research Institute,
University of Texas Health Science Center.
Tenenbaum SA, Lager PJ, Carson CC, Keene JD.
Ribonomics: identifying mRNA subsets in mRNP complexes using
antibodies to RNA-binding proteins and genomic arrays.
Methods. 2002 Feb;26(2):191-8.
Baroni TE, Chittur SV, George AD, Tenenbaum SA.
Advances in RIP-chip analysis : RNA-binding protein
Methods Mol Biol. 2008;419:93-108.
Penalva LO, Tenenbaum SA, Keene JD.
Gene expression analysis of messenger RNP complexes.
Methods Mol Biol. 2004;257:125-34.
Keene JD, Tenenbaum SA.
Eukaryotic mRNPs may represent posttranscriptional operons.
Mol Cell. 2002;9(6):1161-7.
George AD, Tenenbaum SA.
MicroRNA modulation of RNA-binding protein regulatory elements.
RNA Biol. 2006;3(2):57-9. Epub 2006 Apr 1.
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for ENCODE is available