RPmirDIP: Reciprocal Perspective improves miRNA targeting prediction.

Scientific Reports
Daniel G KyrollosJames R Green

Abstract

MicroRNAs (miRNAs) are short, non-coding RNAs that interact with messenger RNA (mRNA) to accomplish critical cellular activities such as the regulation of gene expression. Several machine learning methods have been developed to improve classification accuracy and reduce validation costs by predicting which miRNA will target which gene. Application of these predictors to large numbers of unique miRNA-gene pairs has resulted in datasets comprising tens of millions of scored interactions; the largest among these is mirDIP. We here demonstrate that miRNA target prediction can be significantly improved ([Formula: see text]) through the application of the Reciprocal Perspective (RP) method, a cascaded, semi-supervised machine learning method originally developed for protein-protein interaction prediction. The RP method, aptly named RPmirDIP, augments the original mirDIP prediction scores by leveraging local thresholds from the two complimentary views available to each miRNA-gene pair, rather than apply a traditional global decision threshold. Application of this novel RPmirDIP predictor promises to help identify new, unexpected miRNA-gene interactions. A dataset of RPmirDIP-scored interactions are made available to the scientific com...Continue Reading

References

May 29, 2003·Nucleic Acids Research·Ma Francisca Sánchez-FontGemma Marfany
Dec 19, 2003·Nucleic Acids Research·Sam Griffiths-Jones
Dec 31, 2003·Cell·Benjamin P LewisChristopher B Burge
Mar 12, 2004·Genes & Development·John G Doench, Phillip A Sharp
Sep 24, 2004·RNA·Marc RehmsmeierRobert Giegerich
Oct 27, 2004·PLoS Biology·Bino JohnDebora S Marks
Jun 10, 2005·Nature·Jun LuTodd R Golub
Oct 3, 2006·Developmental Cell·Wigard P Kloosterman, Ronald H A Plasterk
Mar 3, 2007·BMC Bioinformatics·Dimos GaidatzisMihaela Zavolan
May 11, 2007·The Journal of Biological Chemistry·Joachim GeyerErnst Petzinger
Sep 18, 2007·RNA·Cydney B NielsenChristopher B Burge
Sep 26, 2007·Nature Genetics·Michael KerteszEran Segal
Jun 19, 2009·Nature·Sung Wook ChiRobert B Darnell
May 6, 2010·Genome Biology·Mihaela Pertea, Steven L Salzberg
May 15, 2010·BMC Bioinformatics·Isana Veksler-LublinskyMichal Ziv-Ukelson
Jul 21, 2010·Journal of Visualized Experiments : JoVE·Markus HafnerThomas Tuschl
Dec 15, 2010·Nucleic Acids Research·Naama ElefantYael Altuvia
Jun 10, 2011·Nucleic Acids Research·Daniel W ThomsonGregory J Goodall
Jul 28, 2011·BMC Bioinformatics·Justin Bo-Kai HsuHsien-Da Huang
Jan 31, 2012·Bioinformatics·Martin ReczkoArtemis G Hatzigeorgiou
Feb 22, 2012·Genome Research·Vincenzo Alessandro GennarinoSandro Banfi
Oct 5, 2012·Nucleic Acids Research·Charles E Vejnar, Evgeny M Zdobnov
Jan 11, 2013·BMC Genomics·Dong YueYufei Huang
Mar 1, 2014·Nature Protocols·Aleksandra Helwak, David Tollervey
Sep 24, 2014·Molecular Therapy. Nucleic Acids·Gabriella MissoMichele Caraglia
Nov 8, 2014·Genome Research·Hua-Sheng ChiuPavel Sumazin
Nov 8, 2014·Nucleic Acids Research·Nathan Wong, Xiaowei Wang
Jan 7, 2015·BMC Genomics·Daniel Tabas-MadridAlberto Pascual-Montano
Jan 24, 2015·Scientific Reports·Sanghamitra BandyopadhyayZhongming Zhao
Apr 22, 2015·Proceedings of the National Academy of Sciences of the United States of America·Zhiji Ren, Victor R Ambros
Jul 29, 2015·Frontiers in Immunology·Samuel C ForsterPaul J Hertzog
Aug 13, 2015·ELife·Vikram AgarwalDavid P Bartel
Jan 29, 2016·International Journal of Molecular Sciences·Gabriel RinnerthalerRichard Greil
Mar 6, 2016·Pathology, Research and Practice·Hui ShiYijiang Chen
Apr 24, 2016·Nucleic Acids Research·Natasha S Latysheva, M Madan Babu
May 22, 2016·Bioinformatics·Jun DingHaiyan Hu

❮ Previous
Next ❯

Methods Mentioned

BETA
immunoprecipitation
transfect
CLIP
HITS-CLIP
CLIP-Seq
cross-linking ligation
feature extraction

Software Mentioned

XGBoost
RFMirTarget
Random
RPmirDIP
PITA
TargetScan
mirDIP
TarPMir
miRAW
RNACentral

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.