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Turkish Journal of Biochemistry

Türk Biyokimya Dergisi

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IMPACT FACTOR 2016: 0.216
5-year IMPACT FACTOR: 0.323

CiteScore 2016: 0.33

SCImago Journal Rank (SJR) 2016: 0.139
Source Normalized Impact per Paper (SNIP) 2016: 0.296

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1303-829X
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Robust background normalization method for one-channel microarrays

Tek-kanallı mikrodizinlerde sağlam ardalan normalizasyon metodu

Tülay Akal / Vilda Purutçuoğlu / Gerhard-Wilhelm Weber
Published Online: 2017-01-20 | DOI: https://doi.org/10.1515/tjb-2016-0231

Abstract

Background:

Microarray technology, aims to measure the amount of changes in transcripted messages for each gene by RNA via quantifying the colour intensity on the arrays. But due to the different experimental conditions, these measurements can include both systematic and random erroneous signals. For this reason, we present a novel gene expression index, called multi-RGX (Multiple-probe Robust Gene Expression Index) for one-channel microarrays.

Methods:

Multi-RGX, different from other gene expression indices, considers the long-tailed symmetric (LTS) density, covering a wider range of distributions for modelling gene expressions on the log-scale, resulting in robust inference and it takes into account both probe and gene specific intensities. Furthermore, we derive the covariance-variance matrix of model parameters from the observed Fisher information matrix and test the performance of the multi-RGX method in three different datasets.

Results:

Our method is found to be a promising method regarding its alternatives in terms of accuracy and computational time.

Conclusion:

Multi-RGX gives accurate results with respect to its alternatives, with a reduction in computational cost.

Özet

Genel bilgi:

Hesaplamalı biyoloji, biyoteknoloji, biyoenformatik ve tıp bilimlerindeki yeni ve gelişmiş araçlardan biri olan mikrodizin teknolojisi, RNA tarafından her bir gen için transkrip edilen mesajdaki değişim miktarını, dizinlerdeki renk yoğunluğunu bularak ölçmeyi amaçlamaktadır. Fakat farklı deneysel koşullardan dolayı, bu ölçümler hem sistematik hem de rassal hatalı sinyalleri de içerebilir. Bu amaçla, çoklu-RGX (Çoklu Prob-Sağlam Gen İfade İndeksi) adlı, tek-koşullu dizinler için geliştirilmiş, yeni bir gen ifade indeksi sunmaktayız.

Metod:

Diğer indekslerden farklı olarak çoklu-RGX, logaritmik ölçeklerde gen ifadelerinin modellenmesinde daha geniş bir yelpazeyi kapsayan uzun kuyruklu simetrik (LTS) dağılımlı ifadeleri kullanarak dirençli çıkarım olanağı sunmakta ve ölçümlerin tanımlanmasında her bir gen ve her bir probdaki tüm gen ifadelerini göz önüne almaktadır. Ayrıca gözlemlenen Fisher bilgi matrisi yardımıyla, model parametrelerinin varyans-kovaryans matrisini çıkarmakta ve çoklu-RGX’in performansını ölçmek amacıyla, 59 dizin, 10.864 prob çifti ve 11 gen içeren Affymetrix bencmark ve iki tane simüle edilmiş olmak üzere üç farklı veri kümesi kullanmaktayız.

Bulgular:

Metodumuz doğruluk ve hesaplama zamanı açısından alternatiflerine göre güvenilir bulunmuştur.

Sonuç:

Çoklu-RGX alternatifleriyle karşılaştırıldığında hesaplama zamanını kısaltmakla beraber doğru sonuçlar da vermektedir.

Keywords: Gene expression index; Oligonucleotide; Modified maximum likelihood approach; Observed Fisher information matrix; Bioinformatics

Anahtar kelimeler: Gen ifade indeksi; Oligonukleotid; Uyarlanmış en yüksek olabilirlik yöntemi; Gözlemlenen Fisher bilgi matrisi; Biyoenformatik

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About the article

Received: 2016-02-04

Accepted: 2016-06-23

Published Online: 2017-01-20


Conflict of interest statement: There are no conflicts of interest among the authors.


Citation Information: Turkish Journal of Biochemistry, Volume 42, Issue 2, Pages 111–121, ISSN (Online) 1303-829X, ISSN (Print) 0250-4685, DOI: https://doi.org/10.1515/tjb-2016-0231.

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