Missing value estimation for DNA microarray gene expression data: local least squares imputation

Bioinformatics
Hyunsoo KimHaesun Park

Abstract

Gene expression data often contain missing expression values. Effective missing value estimation methods are needed since many algorithms for gene expression data analysis require a complete matrix of gene array values. In this paper, imputation methods based on the least squares formulation are proposed to estimate missing values in the gene expression data, which exploit local similarity structures in the data as well as least squares optimization process. The proposed local least squares imputation method (LLSimpute) represents a target gene that has missing values as a linear combination of similar genes. The similar genes are chosen by k-nearest neighbors or k coherent genes that have large absolute values of Pearson correlation coefficients. Non-parametric missing values estimation method of LLSimpute are designed by introducing an automatic k-value estimator. In our experiments, the proposed LLSimpute method shows competitive results when compared with other imputation methods for missing value estimation on various datasets and percentages of missing values in the data. The software is available at http://www.cs.umn.edu/~hskim/tools.html hpark@cs.umn.edu

References

Aug 30, 2000·Nature·C M PerouD Botstein
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·O AlterD Botstein
Jan 11, 2000·Nucleic Acids Research·G SherlockJ M Cherry
Jun 8, 2001·Bioinformatics·O TroyanskayaR B Altman
Aug 2, 2001·Biochemical and Biophysical Research Communications·I TakemasaK Matsubara
Feb 2, 2002·Nature·Laura J van 't VeerStephen H Friend
Mar 13, 2003·Proceedings of the National Academy of Sciences of the United States of America·Orly AlterDavid Botstein
Nov 5, 2003·Bioinformatics·Shigeyuki ObaShin Ishii
Feb 24, 2004·Nucleic Acids Research·Trond Hellem BøInge Jonassen

❮ Previous
Next ❯

Citations

Aug 17, 2012·Journal of Chemical Information and Modeling·Kathrin HeikampJürgen Bajorath
Apr 30, 2008·Journal of Proteome Research·Xiuxia DuMary S Lipton
Oct 16, 2012·Nature Methods·Yoni DonnerDaphne Koller
Mar 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Juliette Blanchet, Matthieu Vignes
Sep 17, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tobias PetriRalf Zimmer
Aug 25, 2005·Bioinformatics·Rebecka JörnstenMing Ouyang
Dec 27, 2005·Bioinformatics·Johannes TuikkalaTero Aittokallio
Feb 20, 2007·Bioinformatics·Dorothy S V WongGraham R Wood
Mar 9, 2007·Bioinformatics·Wolfram StackliesJoachim Selbig
Nov 14, 2006·Journal of Bioinformatics and Computational Biology·Zhipeng CaiGuohui Lin
Jan 1, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Youting SunEdward R Dougherty
Feb 19, 2009·EURASIP Journal on Bioinformatics & Systems Biology·Muhammad Shoaib B SehgalRoss Coppel
Oct 14, 2009·BMC Bioinformatics·Shweta S ChavanRadhakrishnan Nagarajan
Apr 22, 2010·BMC Bioinformatics·Colm RyanPádraig Cunningham
Sep 28, 2005·BMC Bioinformatics·Brian D M TomJames W Ajioka
Jun 20, 2006·BMC Bioinformatics·Peter Johansson, Jari Häkkinen
Jul 15, 2006·BMC Bioinformatics·Peter D WentzellMargaret Werner-Washburne
Oct 14, 2006·BMC Bioinformatics·Jianjun HuXianghong Jasmine Zhou
Mar 31, 2007·BMC Bioinformatics·Rebecka JörnstenHui-Yu Wang
May 12, 2007·BMC Bioinformatics·Dankyu YoonTaesung Park
Apr 22, 2008·BMC Bioinformatics·Johannes TuikkalaTero Aittokallio
Jun 23, 2006·BMC Medical Informatics and Decision Making·Peyman Jafari, Francisco Azuaje
Feb 26, 2014·BMC Systems Biology·Hsiuying WangWei-Sheng Wu
Mar 3, 2011·PloS One·Espen EnerlyAnne-Lise Børresen-Dale
Nov 14, 2013·Advances in Bioinformatics·Sreevidya Sadananda Sadasiva RaoJeffrey C Miecznikowski
Nov 30, 2005·Proceedings of the National Academy of Sciences of the United States of America·Orly Alter, Gene H Golub
Jun 21, 2007·Critical Reviews in Biotechnology·Lei NieWeiwen Zhang

❮ 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.