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On Recovery of Sparse Signals in Compressed DNA Microarrays

Vikalo, H. and Parvaresh, F. and Hassibi, B. (2007) On Recovery of Sparse Signals in Compressed DNA Microarrays. In: Conference Record of the Forty-First Asilomar Conference on Signals, Systems and Computers, 2007. ACSSC 2007. IEEE , Piscataway, NJ, pp. 693-697. ISBN 978-1-4244-2109-1. https://resolver.caltech.edu/CaltechAUTHORS:20150225-071034629

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Abstract

Currently, DNA micro arrays comprising tens of thousands of probe spots are employed to test entire genomes in a single experiment. Typically, each microarray spot contains a large number of copies of a single probe, and hence collects only a single data point. This is a wasteful use of the sensing resources in comparative DNA microarray experiments, where a test sample is measured relative to a reference sample. Since only a small fraction of the total number of genes represented by the two samples is differentially expressed, a large fraction of a microarray does not provide any useful information. To this end, in this paper we consider an alternative microarray design wherein each spot is a composite of several different probes, and the total number of spots is potentially much smaller than the number of genes being tested. Fewer spots directly translates to significantly lower costs due to cheaper array manufacturing, simpler image acquisition and processing, and smaller amount of genomic material needed for experiments. To recover signals from compressed microarray measurements, we leverage ideas from compressive sampling. Experimental verification of the proposed methodology is presented.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1109/ACSSC.2007.4487303DOIArticle
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=4487303PublisherArticle
Additional Information:© 2007 IEEE. This work was supported in part by a Grubstake Award from California Institute of Technology, a grant from the David and Lucille Packard Foundation, and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech.
Funders:
Funding AgencyGrant Number
Grubstake Award from California Institute of TechnologyUNSPECIFIED
David and Lucille Packard FoundationUNSPECIFIED
Millard and Muriel Jacobs Genetics and Genomics Laboratory at CaltechUNSPECIFIED
DOI:10.1109/ACSSC.2007.4487303
Record Number:CaltechAUTHORS:20150225-071034629
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20150225-071034629
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:55169
Collection:CaltechAUTHORS
Deposited By: Shirley Slattery
Deposited On:27 Feb 2015 01:20
Last Modified:10 Nov 2021 20:42

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