Description

This track shows expression of target RNA binding proteins (RBPs) as measured by RNA-binding protein immunoprecipitation-microarray profiling (RIP-chip) using different RIP antibodies in multiple cell lines. 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:

RBP Assoc RNA

The RBP Assoc RNA view shows the genomic extent of the transcripts associated with the Affymetrix Exon Array probes, shaded according to score.

Methods

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 here.

Credits

These data were produced and analyzed by a collaboration between the Tenenbaum lab 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.

Contact: Scott Tenenbaum

References

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 immunoprecipitation-microarray profiling. 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.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.