Effect of data normalization on fuzzy clustering of DNA microarray data

BMC Bioinformatics
Seo Young KimJong Sung Bae

Abstract

Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. Clustering is an important tool for finding groups of genes with similar expression patterns in microarray data analysis. However, hard clustering methods, which assign each gene exactly to one cluster, are poorly suited to the analysis of microarray datasets because in such datasets the clusters of genes frequently overlap. In this study we applied the fuzzy partitional clustering method known as Fuzzy C-Means (FCM) to overcome the limitations of hard clustering. To identify the effect of data normalization, we used three normalization methods, the two common scale and location transformations and Lowess normalization methods, to normalize three microarray datasets and three simulated datasets. First we determined the optimal parameters for FCM clustering. We found that the optimal fuzzification parameter in the FCM analysis of a microarray dataset depended on the normalization method applied to the dataset during preprocessing. We a...Continue Reading

References

Aug 14, 1998·Molecular Cell·R J ChoR W Davis
Oct 23, 1998·Science·S ChuI Herskowitz
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·P TamayoT R Golub
Jul 3, 1999·Nature Genetics·S TavazoieG M Church
Jun 5, 2001·Nature Reviews. Genetics·J Quackenbush
Jan 17, 2002·Functional & Integrative Genomics·K Zhang, H Zhao
May 23, 2003·Bioinformatics·Doulaye Dembélé, Philippe Kastner
Feb 28, 2004·Bioinformatics·Nabil BelacelRodney Ouellette
Dec 14, 2004·BMC Bioinformatics·John A BergerJaakko Astola
Feb 15, 2005·BMC Bioinformatics·Yingdong ZhaoRichard Simon

❮ Previous
Next ❯

Citations

Oct 14, 2011·Amino Acids·Indrajit SahaDariusz Plewczynski
Jan 22, 2009·BMC Bioinformatics·Ujjwal MaulikSanghamitra Bandyopadhyay
Dec 7, 2007·Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan·Hajime Watanabe
Jun 13, 2017·Computational Statistics & Data Analysis·Shengtong HanHasan Arshad
Nov 26, 2008·Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine·Lixin HanHong Yan
Mar 26, 2009·Journal of Proteome Research·Mihaela E SardiuMichael P Washburn

❮ Previous
Next ❯

Software Mentioned

MathType
R

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Bioinformatics
Doulaye Dembélé, Philippe Kastner
Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
Lixin HanHong Yan
Journal of Bioinformatics and Computational Biology
Matthias E Futschik, Bronwyn Carlisle
IEEE Transactions on Bio-medical Engineering
Patrick C H Ma, Keith C C Chan
© 2021 Meta ULC. All rights reserved