MiRDR-OSG: MicroRNA dynamic regulation analysis utilizing open science grid

Jiang Shu, Juan Cui

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

MicroRNA is a type of short non-coding RNAs, which post-transcriptionally regulate gene expressions. It has been well-documented that human microRNAs contribute in the disease development, such as cancers and obesity. While most microRNA functional studies heavily rely on the regulatory interactions between microRNAs and their target messenger RNAs, the accumulating evidence has shown that the altered availability of microRNAs, their target, and other types of endogenous RNAs competing are able to affect the microRNA-target interactions efficiently, which reflects the dynamic and conditional property of microRNA-mediated gene regulation. Here we present a new computational pipeline, miRDR-OSG, that utilizing the high-throughput computing resource provided by Open Science Grid to study the dynamic regulation of microRNAs in cancer development with the consideration of both competing and cooperative mechanisms. A large-scale genomic dataset from over four thousand patients with 9 major types of cancer was used to demonstrate the usage of miRDR-OSG. As a result, we identified 10,726 microRNA regulatory interactions that only occurred in a specific stage and/or cancer type. This observation demonstrated the dynamic and conditional microRNA regulation during cancer progression. miRDR-OSG is freely available at http://sbbi.unl.edu/miRDR.

Original languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
EditorsIllhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1846-1851
Number of pages6
ISBN (Electronic)9781509030491
DOIs
StatePublished - Dec 15 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: Nov 13 2017Nov 16 2017

Publication series

NameProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume2017-January

Other

Other2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
CountryUnited States
CityKansas City
Period11/13/1711/16/17

Keywords

  • MicroRNA
  • MicroRNA in cancer
  • Open science grid
  • meta-LASSO regression
  • microRNA-mediated gene regulation

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Fingerprint Dive into the research topics of 'MiRDR-OSG: MicroRNA dynamic regulation analysis utilizing open science grid'. Together they form a unique fingerprint.

Cite this