A novel approach for high-quality microarray processing using third-dye array visualization technology

IEEE Transactions on Nanobioscience
Xujing WangMartin J Hessner

Abstract

Historically, microarray image processing has been technically challenging in obtaining quality gene expression data. After hybridization of Cy3- and Cy5-labeled samples, images are collected and processed to obtain gene expression ratio measurements for each of the elements on the array. The hybridization process often brings in contaminating noise, which can make correct identification of the signal difficult. In addition, spot intensity levels are highly variable due to the expression differences of different genes, and weak spots are often difficult to detect. These conditions are further complicated by inherent irregularities in spot position, shape, and size commonly found on high-density microarrays, making image processing an often labor-intensive task that is difficult to reliably automate. We previously reported a novel third-dye array visualization (TDAV) technology that allows prehybridization visualization and quality control of printed arrays. Here, we present a new microarray image processing approach utilizing TDAV. By incorporating the third-dye image, we show that overall quality of the microarray data is significantly improved, and automation of processing is feasible and reliable. Furthermore, we demonstrate...Continue Reading

References

Jan 23, 1999·Nature Genetics·P O Brown, D Botstein
Jan 23, 1999·Nature Genetics·C Debouck, P N Goodfellow
Feb 29, 2000·Nature·A BrazmaM Ashburner
Apr 25, 2000·Nucleic Acids Research·J SchuchhardtH Herzel
May 12, 2000·JAMA : the Journal of the American Medical Association·M DiehnP O Brown
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·T IdekerL E Hood
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M K KerrG A Churchill
Jun 5, 2001·Nature Reviews. Neuroscience·D H Geschwind
Jul 27, 2001·Nucleic Acids Research·J C Mills, J I Gordon
Aug 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·C S BrownP K Sorger
Aug 3, 2001·Nature Cell Biology·J C MillsJ I Gordon
Jan 26, 2002·Briefings in Bioinformatics·Y H YangT P Speed
Feb 6, 2002·Genome Research·Ajay N JainDaniel Pinkel
Feb 28, 2002·Combinatorial Chemistry & High Throughput Screening·Yanbin LiuRichard H Himes
Feb 13, 2003·Nucleic Acids Research·Martin J HessnerSoumitra Ghosh
Oct 1, 1997·Journal of Biomedical Optics·Y ChenM L Bittner

❮ Previous
Next ❯

Citations

Jul 29, 2006·Pediatric Clinics of North America·Martin J HessnerAnne E Kwitek
May 16, 2006·Trends in Biotechnology·Jin-Woo Bae, Yong-Ha Park
Jan 15, 2008·Journal of Molecular and Cellular Cardiology·C E HugginsL M D Delbridge
Sep 21, 2005·Brazilian Journal of Medical and Biological Research = Revista Brasileira De Pesquisas Médicas E Biológicas·V de Mello-Coelho, K L Hess
Sep 21, 2005·The Analyst·Peter D Wentzell, Tobias K Karakach

❮ Previous
Next ❯

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.