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On Methods for the Suppression of Al...

McKenzie, Alex.

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On Methods for the Suppression of Aliasing in Time-Series Gene Expression Data.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	On Methods for the Suppression of Aliasing in Time-Series Gene Expression Data./
Author:	McKenzie, Alex.
Description:	123 p.
Notes:	Source: Masters Abstracts International, Volume: 49-04, page: 2560.
Contained By:	Masters Abstracts International49-04.
Subject:	Engineering, Computer. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=MR71517
ISBN:	9780494715178

On Methods for the Suppression of Aliasing in Time-Series Gene Expression Data.
McKenzie, Alex.

On Methods for the Suppression of Aliasing in Time-Series Gene Expression Data. - 123 p.

Source: Masters Abstracts International, Volume: 49-04, page: 2560.

Thesis (M.A.Sc.)--Carleton University (Canada), 2010.

Gene regulatory networks are an important topic in molecular biology, and their discovery is an area of great activity. Time Series Gene Expression Studies (TSGES), in which multiple sequential measurements of Messenger RNA (mRNA) levels are made to elucidate these networks, are complicated by the extremely high cost of mRNA measurements.

ISBN: 9780494715178Subjects--Topical Terms:

1669061
Engineering, Computer.

On Methods for the Suppression of Aliasing in Time-Series Gene Expression Data.
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100 1 $a McKenzie, Alex. $3 1679380
245 1 0 $a On Methods for the Suppression of Aliasing in Time-Series Gene Expression Data.
300 $a 123 p.
500 $a Source: Masters Abstracts International, Volume: 49-04, page: 2560.
502 $a Thesis (M.A.Sc.)--Carleton University (Canada), 2010.
520 $a Gene regulatory networks are an important topic in molecular biology, and their discovery is an area of great activity. Time Series Gene Expression Studies (TSGES), in which multiple sequential measurements of Messenger RNA (mRNA) levels are made to elucidate these networks, are complicated by the extremely high cost of mRNA measurements.
520 $a The high cost of mRNA measurements necessarily limits the number of samples that can be measured in a single experiment. For an experiment of fixed duration, a limited number of measurements implies a minimum sampling interval, which has the potential to violate the Nyquist criterion. In this thesis a simulation of the GAL regulon in Saccharomyces cerevisiae ( S. cerevisiae) was used to demonstrate that signal corruption from aliasing of high-frequency signal components is possible.
520 $a Effective signal analysis under conditions of restricted sensing is a well-studied area in digital signal processing, and the lessons learned there can be usefully applied to biological research. In particular, the techniques of jitter sampling and Time Aggregation and Skip Sampling (TASS) have great potential to reduce data distortion due to aliasing.
520 $a In jitter sampling, the actual time each measurement is taken is deviated by a small, random amount from the nominal periodic sampling time. Since the probability of the contribution of an above-Nyquist criterion frequency exactly matching all of a number of small, stochastic deviations is vanishingly small, signal contributions which would otherwise be aliased are suppressed. This technique was tested against both a simple sinusoidal data model and the above-mentionned GAL regulon simulation. These tests confirmed that jitter sampling could remove in excess of half of the aliased content of a signal: in one case, an aliased signal was reduced to 25% of the intensity of a non-aliased signal originally of equal magnitude. Furthermore, jitter sampling was demonstrated to be effective with as few as ten samples and when applied to biological systems.
520 $a TASS, in which a cluster of multiple samples are taken in temporal proximity to each primary measurement timepoint and averaged together, is also applicable. Rapid variations in the underlying signal are "averaged out", suppressing high frequency components of the signal. While it is very expensive to measure mRNA levels, the collection of additional physical samples is nearly free. In a biological context, therefore, averaging can be done at very low cost by physically mixing samples together before measuring mRNA levels. Like jitter sampling, TASS was tested on both simplistic and realistic simulated data. One implementation of TASS was able to reduce the aliased signal intensity by 98% relative to the unaliased signal. This technique was also effective with few samples and in biological systems.
520 $a TASS and jitter sampling, while accomplishing similiar objectives, have marked differences and the choice between them is non-trivial. Jitter sampling is simpler to implement and more selective in effect than TASS, but it is counterintuitive and can be unpredictable. Implementing TASS can be more complex and costly, and a poor choice of parameters can result in either inadequate or excessive suppression; on the other hand, TASS is predictable and easy to understand.
590 $a School code: 0040.
650 4 $a Engineering, Computer. $3 1669061
650 4 $a Engineering, Biomedical. $3 1017684
650 4 $a Biology, Bioinformatics. $3 1018415
690 $a 0464
690 $a 0541
690 $a 0715
710 2 $a Carleton University (Canada). $3 1018407
773 0 $t Masters Abstracts International $g 49-04.
790 $a 0040
791 $a M.A.Sc.
792 $a 2010
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=MR71517