A regression-based differential expression detection algorithm for microarray studies with ultra-low sample size

PloS One
Daniel VasiliuMargaret Saha

Abstract

Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED). Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method t...Continue Reading

References

Sep 26, 2003·Cancer Biology & Therapy·Sunil SinghalSteven M Albelda
Feb 13, 2004·Bioinformatics·Ulisses M Braga-Neto, Edward R Dougherty
Jun 23, 2004·Biostatistics·Ji Zhu, Trevor Hastie
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Nov 9, 2004·Bioinformatics·Gersende Fort, Sophie Lambert-Lacroix
May 13, 2005·Statistics in Medicine·Charles KooperbergJames M Olson
Sep 7, 2005·Statistics in Medicine·Hans C van HouwelingenLodewyk F A Wessels
Oct 19, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Li Shen, Eng Chong Tan
Apr 13, 2007·Biostatistics·Mee Young Park, Trevor Hastie
Jun 8, 2007·Bioinformatics·H M BøvelstadO C Lingjaerde
Jun 20, 2008·Briefings in Bioinformatics·Shuangge Ma, Jian Huang
May 2, 2009·Nucleic Acids Research·John Atkinson, Peter McGlynn
Nov 4, 2009·Nucleic Acids Research·Jeff B BowesPeter D Vize
Jul 9, 2010·Bioinformatics·Di WuGordon K Smyth
Jul 24, 2010·Methods in Molecular Biology·Madhu MazumdarHeather L Van Epps
Feb 18, 2011·Biometrical Journal. Biometrische Zeitschrift·Harald BinderMartin Schumacher
Mar 9, 2011·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Gwendolyn E KaeserMargaret S Saha
Jan 4, 2012·Clinical and Translational Science·Kouros OwzarSin-Ho Jung
Mar 1, 2012·Seminars in Cell & Developmental Biology·Angeliki Louvi, Spyros Artavanis-Tsakonas
Mar 7, 2012·Cellular and Molecular Life Sciences : CMLS·Krisztián PappJózsef Prechl
Oct 30, 2012·Cell·Jakob LovénRichard A Young
Nov 19, 2013·Wiley Interdisciplinary Reviews. Computational Statistics·Eric Bair

❮ Previous
Next ❯

Citations

Aug 31, 2017·Scientific Reports·Evani Radiya-DixitAndrew H Beck
Mar 30, 2019·Breast Cancer Research : BCR·Julia Santucci-PereiraJose Russo
Jul 16, 2021·Frontiers in Molecular Neuroscience·Rithvik R NalamalapuMargaret S Saha

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
in vitro transcription
chip

Software Mentioned

R
MATLAB script
MATLAB package
PED
R package “ monomvn ”
MATLAB Bioinformatics Toolbox
Bioconductor
generate
DataMatrix
Octave

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.