miRge 2.0 for comprehensive analysis of microRNA sequencing data

BMC Bioinformatics
Yin LuMarc K Halushka

Abstract

miRNAs play important roles in the regulation of gene expression. The rapidly developing field of microRNA sequencing (miRNA-seq; small RNA-seq) needs comprehensive, robust, user-friendly and standardized bioinformatics tools to analyze these large datasets. We present miRge 2.0, in which multiple enhancements were made towards these goals. miRge 2.0 has become more comprehensive with increased functionality including a novel miRNA detection method, A-to-I editing analysis, integrated standardized GFF3 isomiR reporting, and improved alignment to miRNAs. The novel miRNA detection method uniquely uses both miRNA hairpin sequence structure and composition of isomiRs resulting in higher specificity for potential miRNA identification. Using known miRNA data, our support vector machine (SVM) model predicted miRNAs with an average Matthews correlation coefficient (MCC) of 0.939 over 32 human cell datasets and outperformed miRDeep2 and miRAnalyzer regarding phylogenetic conservation. The A-to-I editing detection strongly correlated with a reference dataset with adjusted R2 = 0.96. miRge 2.0 is the most up-to-date aligner with custom libraries to both miRBase v22 and MirGeneDB v2.0 for 6 species: human, mouse, rat, fruit fly, nematode a...Continue Reading

References

Jun 10, 2005·Nature·Jun LuTodd R Golub
Feb 1, 2006·Trends in Genetics : TIG·V Narry Kim, Jin-Wu Nam
May 18, 2007·Annual Review of Cell and Developmental Biology·Natascha Bushati, Stephen M Cohen
Feb 14, 2008·Nature Reviews. Molecular Cell Biology·Giovanni Stefani, Frank J Slack
Oct 14, 2008·Genome Research·Florian KuchenbauerR Keith Humphries
Oct 29, 2008·Genome Research·Robin C FriedmanDavid P Bartel
Mar 4, 2009·Nature Cell Biology·Julia WinterSven Diederichs
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Mar 3, 2010·Annual Review of Biochemistry·Kazuko Nishikura
Feb 1, 2011·Briefings in Bioinformatics·Melissa J HubiszAdam Siepel
Sep 14, 2011·Nucleic Acids Research·Marc R FriedländerNikolaus Rajewsky
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
Apr 14, 2012·Genome Research·Shahar AlonEli Eisenberg
Aug 14, 2012·Trends in Genetics : TIG·Corine T NeilsenCameron P Bracken
Aug 14, 2012·Methods : a Companion to Methods in Enzymology·Markus HafnerThomas Tuschl
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Feb 26, 2015·Proceedings of the National Academy of Sciences of the United States of America·Eric LondinIsidore Rigoutsos
Apr 17, 2015·Database : the Journal of Biological Databases and Curation·Jing GongAn-Yuan Guo
Jul 15, 2015·Advances in Bioinformatics·Zena M Hira, Duncan F Gillies
Dec 5, 2015·Nucleic Acids Research·Christina BackesAndreas Keller
Oct 30, 2016·RNA Biology·Kenneth W Witwer, Marc K Halushka
Sep 8, 2017·Genome Research·Matthew N McCallMarc K Halushka
Jan 24, 2018·Trends in Genetics : TIG·Marc K HalushkaMatthew N McCall

❮ Previous
Next ❯

Citations

May 23, 2019·Nucleic Acids Research·Ernesto Aparicio-PuertaMichael Hackenberg
Jun 3, 2020·Nucleic Acids Research·Ernesto Aparicio-PuertaMichael Hackenberg
Sep 11, 2019·Bioinformatics·Thomas DesvignesLorena Pantano
Dec 15, 2019·International Journal of Molecular Sciences·Marta Correia de SousaMichelangelo Foti
Jul 12, 2020·Cancers·Giulia RomanoPatrick Nana-Sinkam
Sep 27, 2020·Proceedings of the National Academy of Sciences of the United States of America·Alina IsakovaStephen R Quake
Sep 23, 2020·The Journal of Infectious Diseases·Monika M LooneyMarc K Halushka
Dec 15, 2020·Briefings in Bioinformatics·Georges Pierre SchmartzAndreas Keller
Jan 6, 2021·Genes·Athanasios AlexiouArtemis G Hatzigeorgiou
Apr 20, 2021·Nucleic Acids Research·Tobias FehlmannAndreas Keller
May 1, 2021·Cancers·Gioacchino P MarcecaGiovanni Nigita
May 13, 2021·Nature Communications·Sungsam GongD Stephen Charnock-Jones
Jun 23, 2021·Investigative Ophthalmology & Visual Science·Wouter H G HubensTheo G M F Gorgels
Jul 27, 2021·NAR Genomics and Bioinformatics·Arun H Patil, Marc K Halushka
Jan 16, 2021·The European Respiratory Journal·Kevin M MagnayeCarole Ober

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRR944034
SRR3653310
SRR5241768
ERR409900
SRR837842
SRR553572
SRR837839
SRR1646493
DKS8

Methods Mentioned

BETA
RNA-seq

Software Mentioned

miRge
Bowtie
cutadapt
PHAST
PhyloP
RNAfold
miRTop
numPy
sklearn
bcbio

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.