A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification

BMC Genomics
Shanrong Zhao, Baohong Zhang

Abstract

RNA-Seq has become increasingly popular in transcriptome profiling. One aspect of transcriptome research is to quantify the expression levels of genomic elements, such as genes, their transcripts and exons. Acquiring a transcriptome expression profile requires genomic elements to be defined in the context of the genome. Multiple human genome annotation databases exist, including RefGene (RefSeq Gene), Ensembl, and the UCSC annotation database. The impact of the choice of an annotation on estimating gene expression remains insufficiently investigated. In this paper, we systematically characterized the impact of genome annotation choice on read mapping and transcriptome quantification by analyzing a RNA-Seq dataset generated by the Human Body Map 2.0 Project. The impact of a gene model on mapping of non-junction reads is different from junction reads. For the RNA-Seq dataset with a read length of 75 bp, on average, 95% of non-junction reads were mapped to exactly the same genomic location regardless of which gene models was used. By contrast, this percentage dropped to 53% for junction reads. In addition, about 30% of junction reads failed to align without the assistance of a gene model, while 10-15% mapped alternatively. There a...Continue Reading

References

Feb 28, 2006·Bioinformatics·Fan HsuDavid Haussler
Aug 24, 2006·Genome Biology·Danielle Thierry-Mieg, Jean Thierry-Mieg
Nov 16, 2007·Nucleic Acids Research·L G WilmingJ L Harrow
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Jun 19, 2009·Briefings in Functional Genomics & Proteomics·Paul J Hurd, Christopher J Nelson
Feb 12, 2010·Bioinformatics·Thomas D Wu, Serban Nacu
Mar 12, 2010·Nature·Stephen B MontgomeryEmmanouil T Dermitzakis
Aug 31, 2010·Nucleic Acids Research·Kai WangJinze Liu
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
May 31, 2011·Nature Methods·Manuel GarberCole Trapnell
Jun 2, 2011·BMC Biology·John H Malone, Brian Oliver
May 18, 2012·Bioinformatics·Jun HuKejun Liu
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
Oct 2, 2012·Current Opinion in Biotechnology·Kai-Oliver MutzFrank Stahl
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Mar 19, 2013·BMC Bioinformatics·Charlotte Soneson, Mauro Delorenzi
Nov 5, 2013·Nature Methods·Pär G EngströmUNKNOWN RGASP Consortium
Dec 10, 2013·Nucleic Acids Research·Paul FlicekStephen M J Searle

❮ Previous
Next ❯

Citations

Dec 15, 2015·Bioinformatics·Youri HoogstrateAndrew P Stubbs
Jan 28, 2016·Genome Biology·Ana ConesaAli Mortazavi
Sep 10, 2015·Biological Chemistry·Alexander BartholomäusZoya Ignatova
Aug 19, 2015·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Sleiman BassimRejean Tremblay
Mar 21, 2015·Clinical Biochemistry·Cees B M Oudejans
Oct 23, 2016·BMC Bioinformatics·Sergi SayolsHolger Klein
Dec 3, 2016·Nucleic Acids Research·Bronwen L AkenPaul Flicek
Sep 30, 2017·Bioinformatics·Karolina Elzbieta Kaczor-UrbanowiczDavid T W Wong
Feb 27, 2016·Bioinformatics and Biology Insights·Jessica P HekmanAnna V Kukekova
Nov 27, 2015·Bioinformatics and Biology Insights·Yixing HanBing Zhou
Mar 27, 2018·Briefings in Functional Genomics·Christoph ZiegenhainWolfgang Enard
Jul 7, 2018·The Plant Journal : for Cell and Molecular Biology·Oren TzfadiaAsaph Aharoni
Jul 25, 2017·Genetics·Chen ChenMolly Przeworski
Apr 25, 2019·BMC Genomics·Giovanni CarapezzaRoberta Bosotti
Sep 24, 2019·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Klas HatjeMartin Kollmar
Oct 9, 2019·Proceedings of the National Academy of Sciences of the United States of America·Luis P IñiguezMatthew L Bendall
Dec 14, 2019·Bioinformatics·Carlos Martí-GómezFátima Sánchez-Cabo
Jun 5, 2019·Genome Biology·Antonin Morillon, Daniel Gautheret
Oct 13, 2019·Nature Communications·Beate ViethInes Hellmann
Jun 3, 2017·Scientific Reports·Maria KondiliMario Looso
Aug 30, 2018·BMC Genomics·Shamsuddin A BhuiyanPaul Pavlidis
Jun 26, 2017·BMC Genomics·Haibo LiuChristopher K Tuggle
Jan 26, 2020·Nucleic Acids Research·Vincent BoivinMichelle S Scott
Jul 3, 2019·RNA·Luisa M Arake de TaccaJamie H D Cate

❮ Previous
Next ❯

Datasets Mentioned

BETA
E-MTAB-513

Methods Mentioned

BETA
RNA-Seq
RNA-
Seq
chip

Software Mentioned

ArrayExpress
Vega
Ensembl
GSNAP
MapSplice
Tophat
RefGene
RefSeq
OSA
AceView

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.