Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios

Bioinformatics
Emmanuel CurisCynthia Marie-Claire

Abstract

RNA quantification experiments result in compositional data, however usual methods for compositional data analysis [additive log ratio (alr), centered log ratio (clr), isometric log ratio (ilr)] do not apply easily and give results difficult to interpret. To handle this, a method based on disjoint subgraphs in a graph whose nodes are the quantified RNAs is proposed. Edges in the graph are defined by lack of change in ratios of the corresponding RNAs between conditions. The methods is suited for qRT-PCR and RNA-Seq data analyses, and leads to easy-to-interpret, graphical results and the identification of set of genes that share a similar behavior when the studied condition changes. For qRT-PCR data, it has better statistical properties than the common ΔΔCq method. Construction of all pairwise ratio analysis P-values matrix, and conversion into a graph was implemented in an R package, named SARP.compo. It is freely available for download on the CRAN repository. Example R script using the package are provided as Supplementary Material; the R package includes the data needed. One of these scripts reproduces the Figure 2 of this paper. Supplementary data are available at Bioinformatics online.

References

Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Jan 7, 2004·Biochemical and Biophysical Research Communications·Aleksandar RadonićAndreas Nitsche
Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Aaron ClausetCristopher Moore
Aug 16, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Jörg Reichardt, Stefan Bornholdt
Jun 24, 2008·Analytical Biochemistry·Adrian E PlattsStephen A Krawetz
Sep 25, 2008·Analytical Biochemistry·Stefan Cikos, Juraj Koppel
Sep 11, 2009·The Science of the Total Environment·Peter FilzmoserClemens Reimann
Sep 15, 2012·Methods : a Companion to Methods in Enzymology·Jan M RuijterJo Vandesompele
Oct 3, 2012·PLoS Computational Biology·Jonathan Friedman, Eric J Alm
Aug 26, 2014·Nature Biotechnology·Davide RissoSandrine Dudoit
Dec 6, 2014·Clinical Chemistry·Andrej-Nikolai SpiessStefan Rödiger
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
May 5, 2016·Annals of Epidemiology·Gregory B GloorJuan José Egozcue
Jun 4, 2016·Annals of Epidemiology·Matthew C B Tsilimigras, Anthony A Fodor
Jan 28, 2017·World Psychiatry : Official Journal of the World Psychiatric Association (WPA)·Shekhar Saxena, Mario Maj
Feb 16, 2017·ELife·Justin D SilvermanLawrence A David
Aug 11, 2017·European Journal of Clinical Investigation·Stephen Bustin, Tania Nolan

❮ Previous
Next ❯

Citations

Nov 9, 2019·Scientific Reports·Emmanuel CurisCynthia Marie-Claire
Mar 31, 2021·Chronobiology International·D Grillault LarocheC Marie-Claire
Jul 8, 2020·Psychoneuroendocrinology·D Grillault LarocheC Marie-Claire

❮ 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.