By Topic

A Clustering Approach to Identify Intergenic Non-coding RNA in Mouse Macrophages

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

4 Author(s)
Garmire, L.X. ; Dept. of Bioeng., Univ. of California at San Diego, La Jolla, CA, USA ; Subramaniam, S. ; Garmire, D. ; Glass, C.K.

We present a global clustering approach to identify putative intergenic non-coding RNAs based on the RNA polymerase II and Histone 3 lysine 4 trimethylation signatures. Both of these signatures are processed from the digital sequencing tags produced by chromatin immunoprecipitation, a high-throughput massively parallel sequencing (ChIP-Seq) technology. Our method compares favorably to the comparison method. We characterize the intergenic non-coding RNAs to have conservative promoters. We predict that these nc-RNAs are related to metabolic process without lipopolysaccharides (LPS) treatment, but shift towards developmental and immune-related functions with LPS treatment. We demonstrate that more intergenic nc-RNAs respond positively to LPS treatment, rather than negatively. Using QPCR, we experimentally validate 8 out of 11 nc-RNA regions respond to LPS treatment as predicted by the computational method.

Published in:

BioInformatics and BioEngineering (BIBE), 2010 IEEE International Conference on

Date of Conference:

May 31 2010-June 3 2010