Quantile normalization for high throughput circulating MicroRNA expression study using TaqMan® low density array panels: supporting evidence

Ahmad, Azmir and Mohamed, Syarah Syamimi and Tumian, Afidalina and Tolos, Siti Marponga and Sivanesan, Vijaya Mohan and Leman, Wan Ishlah and Abdullah, Kahairi and Mohamad, Irfan and Wan Zainon, Wan Mohd Nazri and Rosla, Luqman and Syed Yussof, Sharifah Nor Ezura and Mark, Paul and Mohamed@Awang, Kamariah and Ramli, Rosdi and Kamar Omar, Eshamsol and Mohd. Yassin, Wardah and Mohamad, Mohd. Amin Marwan and Kaderi, Mohd Arifin (2024) Quantile normalization for high throughput circulating MicroRNA expression study using TaqMan® low density array panels: supporting evidence. HAYATI Journal of Biosciences, 31 (3). pp. 432-442. ISSN 1978-3019 E-ISSN 2086-4094

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Abstract

In searching for new biomarkers, high throughput technique has been widely used by researchers, including for gene expression study. However, the reliability and accuracy of results from high throughput study critically depends on appropriate data management, including normalization methods. Data driven normalization has been introduced as a normalization method for high throughput gene expression study. Thus, this study was conducted to evaluate the performance of various data driven and reference genes normalization methods using a high throughput circulating microRNA expression dataset. A quantification cycle (Cq) dataset generated from a high throughput circulating microRNA study was used to test the normalization methods using HTqPCR package in R software. The normalized Cq generated from different methods were compared descriptively using box plot analysis and coefficient of variance. The box plot analysis showed that quantile normalization produced more homogenous Cq distribution, lesser outliers and reduced coefficient of variance as compared to other normalization methods in screening and validation phases. The overview on quantile normalized Cq showed consistency in its level of expression before and after 2-ΔΔCq calculation indicating the reliability of quantile normalized Cq. Quantile normalization is suggested to be used in high throughput miRNA expression study due to its performance in homogenizing the data, reduce outliers and coefficient of variance.

Item Type:	Article (Journal)
Uncontrolled Keywords:	quantile, normalization, data driven, circulating miRNAs, high throughput
Subjects:	Q Science > QD Chemistry R Medicine > RC Internal medicine > RC254 Neoplasms. Tumors. Oncology (including Cancer) > RC261 Cancer and other malignant neoplasms R Medicine > RF Otorhinolaryngology
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Allied Health Sciences Kulliyyah of Allied Health Sciences > Department of Biomedical Science (Effective:1st July 2011) Kulliyyah of Medicine Kulliyyah of Medicine > Department of Otolaryngology - Head and Neck Surgery Kulliyyah of Nursing Kulliyyah of Nursing > Department of Basic Medical Sciences for Nursing Kulliyyah of Science Kulliyyah of Science > Department of Computational and Theoretical Sciences
Depositing User:	Dr. Azmir Ahmad
Date Deposited:	23 Feb 2024 11:13
Last Modified:	31 Jul 2024 15:11
URI:	http://irep.iium.edu.my/id/eprint/110976

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