Identifying miRNA synergistic regulatory networks in heterogeneous human data via network motifs

Molecular BioSystems
Junpeng ZhangJiuyong Li

Abstract

Understanding the synergism of multiple microRNAs (miRNAs) in gene regulation can provide important insights into the mechanisms of complex human diseases caused by miRNA regulation. Therefore, it is important to identify miRNA synergism and study miRNA characteristics in miRNA synergistic regulatory networks. A number of methods have been proposed to identify miRNA synergism. However, most of the methods only use downstream target genes of miRNAs to infer miRNA synergism when miRNAs can also be regulated by upstream transcription factors (TFs) at the transcriptional level. Additionally, most methods are based on statistical associations identified from data without considering the causal nature of gene regulation. In this paper, we present a causality based framework, called mirSRN (miRNA synergistic regulatory network), to infer miRNA synergism in human molecular systems by considering both downstream miRNA targets and upstream TF regulation. We apply the proposed framework to two real world datasets and discover that almost all the top 10 miRNAs with the largest node degree in the mirSRNs are associated with different human diseases, including cancer, and that the mirSRNs are approximately scale-free and small-world networks...Continue Reading

References

Oct 16, 1999·Science·A L Barabasi, R Albert
Dec 14, 2001·Proceedings of the National Academy of Sciences of the United States of America·S RamaswamyTodd R Golub
Jan 10, 2002·Cell·Victor Ambros
Jan 15, 2003·BMC Bioinformatics·G D Bader, Christopher W V Hogue
Apr 5, 2003·Proceedings of the National Academy of Sciences of the United States of America·Debra S Goldberg, Frederick P Roth
Jan 8, 2004·Genome Biology·Anton J EnrightDebora S Marks
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
Apr 5, 2005·Nature Genetics·Azra KrekNikolaus Rajewsky
Jun 10, 2005·Nature·Jun LuTodd R Golub
Mar 25, 2006·Nature Reviews. Cancer·Aurora Esquela-Kerscher, Frank J Slack
Sep 14, 2006·Molecular Systems Biology·Qinghua CuiEdwin Wang
Jan 19, 2007·Nature Reviews. Genetics·Kevin Chen, Nikolaus Rajewsky
Feb 6, 2007·Bioinformatics·A FerroD Shasha
May 18, 2007·Annual Review of Cell and Developmental Biology·Natascha Bushati, Stephen M Cohen
Aug 19, 2007·Cell Research·Tingting Du, Phillip D Zamore
Nov 10, 2007·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Nov 17, 2007·Bioinformatics·Yassen AssenovMario Albrecht
Oct 17, 2008·PloS One·Ming LuQinghua Cui
Oct 18, 2008·Cell Cycle·Philip A GregoryGregory J Goodall
Oct 29, 2008·Genome Research·Robin C FriedmanDavid P Bartel
Mar 11, 2009·Nature Reviews. Genetics·Juan M VaquerizasNicholas M Luscombe
Jun 30, 2009·BMC Systems Biology·Xiongying YuanYi Zhao
Feb 26, 2010·Journal of Bioinformatics and Computational Biology·Jiyuan AnYi-Ping Phoebe Chen
Apr 1, 2010·Nature Methods·Marloes H MaathuisPeter Bühlmann
May 21, 2010·Nucleic Acids Research·Gabriele SalesChiara Romualdi
Jul 2, 2010·Cancer Biology & Therapy·Perry S Mongroo, Anil K Rustgi
Jan 22, 2011·Molecular Cancer Therapeutics·Rolf SøkildeThomas Litman
Apr 13, 2011·Molecular BioSystems·Debarka Sengupta, Sanghamitra Bandyopadhyay
Jul 28, 2011·BMC Bioinformatics·Justin Bo-Kai HsuHsien-Da Huang
Jan 1, 2011·Brain Connectivity·Qawi K TelesfordPaul J Laurienti
Dec 19, 2012·International Journal of Biological Macromolecules·Xuhai ZhaoXiangshi Lu
May 22, 2013·PloS One·Wenliang ZhuZhimin Du
Dec 30, 2014·PloS One·Gianfranco PolitanoStefano Di Carlo
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Aug 13, 2015·ELife·Vikram AgarwalDavid P Bartel

Citations

Apr 13, 2018·International Journal of Molecular Sciences·Mohsen NavariPier Paolo Piccaluga
Jul 1, 2017·Scientific Reports·Bhaskar RoyYogesh Dwivedi
Dec 29, 2019·BMC Bioinformatics·Junpeng ZhangThuc Duy Le

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.

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.

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.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Separation Anxiety

Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.

KIF1A Associated Neurological Disorder

KIF1A associated neurological disorder (KAND) is a rare neurodegenerative condition caused by mutations in the KIF1A gene. KAND may present with a wide range and severity of symptoms including stiff or weak leg muscles, low muscle tone, a lack of muscle coordination and balance, and intellectual disability. Find the latest research on KAND here.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.