Expression profiling of microRNAs by deep sequencing

Briefings in Bioinformatics
Chad J CreightonPreethi H Gunaratne


MicroRNAs are short non-coding RNAs that regulate the stability and translation of mRNAs. Profiling experiments, using microarray or deep sequencing technology, have identified microRNAs that are preferentially expressed in certain tissues, specific stages of development, or disease states such as cancer. Deep sequencing utilizes massively parallel sequencing, generating millions of small RNA sequence reads from a given sample. Profiling of microRNAs by deep sequencing measures absolute abundance and allows for the discovery of novel microRNAs that have eluded previous cloning and standard sequencing efforts. Public databases provide in silico predictions of microRNA gene targets by various algorithms. To better determine which of these predictions represent true positives, microRNA expression data can be integrated with gene expression data to identify putative microRNA:mRNA functional pairs. Here we discuss tools and methodologies for the analysis of microRNA expression data from deep sequencing.


Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Jun 5, 2001·Nature Reviews. Genetics·J Quackenbush
Feb 20, 2003·RNA·Victor AmbrosThomas Tuschl
Jul 21, 2004·Molecular Cell·Gunter MeisterThomas Tuschl
Jul 31, 2004·Science·Jidong LiuGregory J Hannon
Oct 27, 2004·PLoS Biology·Bino JohnDebora S Marks
Feb 22, 2005·PLoS Biology·Julius BrenneckeStephen M Cohen
Apr 5, 2005·Nature Genetics·Azra KrekNikolaus Rajewsky
Jun 10, 2005·Nature·Jun LuTodd R Golub
Oct 15, 2005·Development·Tingting Du, Phillip D Zamore
Oct 25, 2006·Nature Methods·Praveen SethupathyArtemis G Hatzigeorgiou
Nov 9, 2007·Proceedings of the National Academy of Sciences of the United States of America·J Mauro CalabresePhillip A Sharp
Nov 21, 2007·Nature Methods·Jim C HuangQuaid D Morris
Dec 26, 2007·Methods : a Companion to Methods in Enzymology·Philipp BerningerMihaela Zavolan
Apr 9, 2008·Nature Biotechnology·Marc R FriedländerNikolaus Rajewsky
Jun 5, 2008·Biochemical and Biophysical Research Communications·Sonika TyagiAlok Bhattacharya
Jul 1, 2008·Bioinformatics·Yunpen XuWeixiong Zhang
Aug 1, 2008·Nature·Daehyun BaekDavid P Bartel
Aug 1, 2008·Nature·Matthias SelbachNikolaus Rajewsky
Aug 21, 2008·Bioinformatics·Simon MoxonVincent Moulton
Oct 11, 2008·Nature Biotechnology·Jeffery A Schloss
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Oct 29, 2008·Genome Research·Robin C FriedmanDavid P Bartel

❮ Previous
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Jun 26, 2012·Cancer Metastasis Reviews·N P A Devika GunasingheHonor J Hugo
Aug 30, 2011·Plant Molecular Biology·Guiling Sun
Jul 16, 2011·Hormones & Cancer·Michael A TesselPreethi H Gunaratne
Jun 21, 2012·Journal of Agricultural and Food Chemistry·Qingpo Liu, Hengmu Zhang
Dec 21, 2011·Briefings in Functional Genomics·David J Studholme
Oct 30, 2009·Briefings in Bioinformatics·David Stephen HornerGraziano Pesole
Jan 22, 2013·Briefings in Bioinformatics·Vernell WilliamsonVladimir Vladimirov
Jun 12, 2010·Bioinformatics·Zhang ZhangJeffrey P Townsend
Apr 12, 2012·Carcinogenesis·Marilena V Iorio, Carlo M Croce
Mar 29, 2012·Genome Biology and Evolution·Michael DannemannJanet Kelso
Mar 1, 2013·Journal of Radiation Research·M Ahmad ChaudhryNader Pourmand
May 19, 2010·Nucleic Acids Research·Erle ZhuJinyu Wu
Mar 2, 2012·Nucleic Acids Research·Gong ZhangZoya Ignatova
Jun 19, 2012·Nucleic Acids Research·Chikako RaganDenis C Bauer
Jun 19, 2013·Nucleic Acids Research·David T Humphreys, Catherine M Suter
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Mar 25, 2010·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Jill KoshiolMaria Teresa Landi
Oct 14, 2009·BMC Bioinformatics·Wei-Chi WangNa-Sheng Lin
Dec 21, 2010·BMC Bioinformatics·Clark D JeffriesXiaojun Guan
Dec 22, 2010·BMC Genomics·Marianthi KaraliSandro Banfi
Dec 22, 2010·BMC Genomics·Henk P J BuermansPeter A C 't Hoen
Jun 2, 2011·BMC Genomics·Preethi H GunaratneDavid F Clayton
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