NormQ: RNASeq normalization based on RT-qPCR derived size factors

Computational and Structural Biotechnology Journal
Ravindra NaraineRadek Sindelka

Abstract

The merit of RNASeq data relies heavily on correct normalization. However, most methods assume that the majority of transcripts show no differential expression between conditions. This assumption may not always be correct, especially when one condition results in overexpression. We present a new method (NormQ) to normalize the RNASeq library size, using the relative proportion observed from RT-qPCR of selected marker genes. The method was compared against the popular median-of-ratios method, using simulated and real-datasets. NormQ produced more matches to differentially expressed genes in the simulated dataset and more distribution profile matches for both simulated and real datasets.

References

Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Jan 7, 2010·Methods : a Companion to Methods in Enzymology·Radek SindelkaMikael Kubista
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Aug 6, 2011·Genome Research·Lichun JiangBrian Oliver
Sep 19, 2012·Briefings in Bioinformatics·Marie-Agnès DilliesUNKNOWN French StatOmique Consortium
Oct 17, 2012·Bioinformatics·Evguenia KopylovaHélène Touzet
Oct 30, 2012·Cell·Jakob LovénRichard A Young
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Oct 11, 2013·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Raghu ChandramohanMay D Wang
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Aug 26, 2014·Nature Biotechnology·Davide RissoSandrine Dudoit
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Nov 25, 2014·Cell·Jan Philipp JunkerAlexander van Oudenaarden
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
May 1, 2015·Bioinformatics·Alyssa C FrazeeJeffrey T Leek
Dec 30, 2015·Molecular and Cellular Biology·Kaifu ChenJessica K Tyler
Apr 5, 2016·Nature Biotechnology·Nicolas L BrayLior Pachter
Mar 24, 2017·Briefings in Bioinformatics·Ciaran EvansDaniel M Stoebel
Oct 24, 2017·Nucleic Acids Research·Kamran KarimiPeter D Vize

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE104848
GSE125819

Methods Mentioned

BETA
RNASeq
PCA

Software Mentioned

R package metaseqR
TrimmomaticPE
Simulated
Sortmerna
Trimmomatic
count
BLAST
TOMOSeq
htseq
degCheckFactors

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.