A comparison of analog and Next-Generation transcriptomic tools for mammalian studies

Briefings in Functional Genomics
Nicole C RoyWarren C McNabb

Abstract

This review focuses on tools for studying a cell's transcriptome, the collection of all RNA transcripts produced at a specific time, and the tools available for determining how these changes in gene expression relate to the functional changes in an organism. While the microarray-based (analog) gene-expression profiling technology has dominated the 'omics' era, Next-Generation Sequencing based gene-expression profiling (RNA-Seq) is likely to replace this analog technology in the future. RNA-Seq shows much promise for transcriptomic studies as the genes of interest do not have to be known a priori, new classes of RNA, SNPs and alternative splice variants can be detected, and it is also theoretically possible to detect transcripts from all biologically relevant abundance classes. However, the technology also brings with it new issues to resolve: the specific technical properties of RNA-Seq data differ to those of analog data, leading to novel systematic biases which must be accounted for when analysing this type of data. Additionally, multireads and splice junctions can cause problems when mapping the sequences back to a genome, and concepts such as cloud computing may be required because of the massive amounts of data generated.

References

Nov 1, 1988·Analytical Biochemistry·E D Hyman
Oct 23, 1997·Genome Research·S Audic, J M Claverie
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Mar 31, 2000·Trends in Biotechnology·D W Deamer, M Akeson
Feb 22, 2001·Science·J C VenterX Zhu
Mar 10, 2001·Nature·Eric S LanderInternational Human Genome Sequencing Consortium
Apr 12, 2003·Science·Francis S CollinsAristides Patrinos
Apr 19, 2003·Genome Biology·Xiangqin Cui, Gary A Churchill
Oct 2, 2003·Genome Biology·Douglas A HosackRichard A Lempicki
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
Oct 6, 2004·Genome Biology·Robert GentlemanJianhua Zhang
Oct 22, 2004·Nature·International Human Genome Sequencing Consortium
Apr 6, 2005·Veterinary Immunology and Immunopathology·Robin E EvertsHarris A Lewin
Apr 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Tae Seok SeoJingyue Ju
May 4, 2005·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Paul BertoneMichael Snyder
Aug 4, 2005·Bioinformatics·Claire L Wilson, Crispin J Miller
Sep 29, 2005·Molecular Nutrition & Food Research·Bettina Spielbauer, Frank Stahl
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Dec 22, 2005·Nature Reviews. Genetics·David B AllisonMahyar Sabripour
Jan 10, 2006·BMC Bioinformatics·Ramón Díaz-Uriarte, Sara Alvarez de Andrés
Apr 28, 2006·Nature Genetics·Michael ReichJill P Mesirov
Nov 14, 2006·Bioinformatics·S Falcon, Robert Gentleman
Sep 21, 2007·Bioinformatics·Mark D Robinson, Gordon K Smyth
Oct 27, 2007·BMC Genetics·Stephanie D McKayStephen S Moore
Feb 12, 2008·Trends in Genetics : TIG·Elaine R Mardis
Apr 19, 2008·Journal of Dairy Science·M SargolzaeiL R Schaeffer
May 6, 2008·Reproduction : the Official Journal of the Society for the Study of Fertility·A BonnetG Tosser-Klopp
May 10, 2008·Bioinformatics·Pan DuSimon M Lin
May 21, 2008·BMC Genomics·Heleen M de Vogel-van den BoschM Müller
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara J Wold
Oct 25, 2008·BMC Bioinformatics·Dustin P PotterShili Lin
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Nov 6, 2008·Bioinformatics·Karen KapurWing Hung Wong
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Nov 22, 2008·Science·John EidStephen Turner
Nov 27, 2008·Genes & Nutrition·P J De GrootM Müller
Dec 25, 2008·Bioinformatics·Audrey KauffmannWolfgang Huber
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 6, 2009·Bioinformatics·Yang XieMichael Story
Mar 10, 2009·PloS One·James W KijasInternational Sheep Genomics Consortium
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Mar 31, 2009·Genome Biology·Olivier HarismendyKelly A Frazer
Apr 8, 2009·Nature Nanotechnology·James ClarkeHagan Bayley
Apr 18, 2009·Biology Direct·Alicia Oshlack, Matthew J Wakefield
Apr 25, 2009·PloS One·Lakshmi K MatukumalliCurtis P Van Tassell
May 15, 2009·Journal of Biology·David W Burt
Jul 22, 2009·Nucleic Acids Research·Dmitri ParkhomchukAlexey Soldatov
Sep 1, 2009·Annual Review of Genomics and Human Genetics·Olena MorozovaMarco A Marra
Nov 3, 2009·Nature Methods·Shirley PepkeAli Mortazavi
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
May 5, 2010·Genetics·Paul L Auer, R W Doerge
May 6, 2010·Genome Biology·Lincoln D Stein
Jun 4, 2010·Genome Research·Ana P VivancosHeinz Himmelbauer
Jul 10, 2010·PLoS Computational Biology·Augix Guohua XuPhilipp Khaitovich
Jul 20, 2010·Nature Methods·Fatih OzsolakDaniel A Haber

Citations

Mar 14, 2012·Nature Reviews. Gastroenterology & Hepatology·Lynnette R Ferguson
Jul 24, 2013·Briefings in Functional Genomics·Bryan D HudsonGabriela G Loots
Sep 7, 2013·EURASIP Journal on Bioinformatics & Systems Biology·Guy Karlebach
Jul 12, 2013·PloS One·Andrew D FernandesGregory B Gloor
Jan 25, 2014·General and Comparative Endocrinology·Kristy M LongpreAndrzej Z Pietrzykowski
Jan 9, 2014·Cellular and Molecular Life Sciences : CMLS·Ryoiti Kiyama, Yun Zhu
May 9, 2014·Integrative and Comparative Biology·Carol A Fassbinder-Orth
Sep 13, 2014·Briefings in Functional Genomics·Martha Lucía MeijueiroAntonio G Pisabarro
Aug 9, 2011·Expert Review of Proteomics·Hao HuYuquan Wei
Jan 21, 2014·The Journal of Investigative Dermatology·Bingshan LiJames T Elder
Oct 3, 2015·Computational and Structural Biotechnology Journal·Daniel Spies, Constance Ciaudo
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Noah BerlowRanadip Pal
Dec 4, 2012·Genomics, Proteomics & Bioinformatics·Jiandong DingJihong Guan
Sep 23, 2014·Briefings in Functional Genomics·Francesca Finotello, Barbara Di Camillo
Apr 5, 2015·The Journal of Allergy and Clinical Immunology·Mayte Suárez-FariñasEmma Guttman-Yassky
Jul 31, 2012·Methods : a Companion to Methods in Enzymology·Alison S DevonshireJim F Huggett
Sep 11, 2014·Frontiers in Immunology·Kirsten E McLoughlinDavid E MacHugh
Nov 13, 2012·Toxicologic Pathology·Robert A Ettlin
May 26, 2017·The British Journal of Dermatology·J DouX Zhang
Nov 26, 2016·BMC Veterinary Research·Alessandra CrisàBianca Moioli
Jul 3, 2020·The Journal of Allergy and Clinical Immunology·Lena MöbusTREATgermany study group

Related Concepts

Computer Programs and Programming
Genome
Sequence Determinations, RNA
Cdna Microarrays
MRNA Differential Display
Analogs & derivatives
Gene Expression
Genes
Genome
RNA

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.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Congenital Hyperinsulinism

Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

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.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Cell Atlas of the Human Eye

Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.

Femoral Neoplasms

Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms 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.