TY - GEN
T1 - MiRDR-OSG
T2 - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
AU - Shu, Jiang
AU - Cui, Juan
N1 - Funding Information:
ACKNOWLEDGMENT We appreciate the UNL Holland Computing Center and the Open Science Grid for providing the computational facility. This research is support by the National Institutes of Health funded COBRE grant (grant number 1P20GM104320), UNL Food For Health seed grant and the Tobacco Settlement Fund as part of the Cui’s start-up grant support. Shu received a fellowship from Open Science Grid User School 2016 at University of Wisconsin-Madison.
Publisher Copyright:
© 2017 IEEE.
PY - 2017/12/15
Y1 - 2017/12/15
N2 - 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.
AB - 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.
KW - MicroRNA
KW - MicroRNA in cancer
KW - Open science grid
KW - meta-LASSO regression
KW - microRNA-mediated gene regulation
UR - http://www.scopus.com/inward/record.url?scp=85046101321&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85046101321&partnerID=8YFLogxK
U2 - 10.1109/BIBM.2017.8217941
DO - 10.1109/BIBM.2017.8217941
M3 - Conference contribution
AN - SCOPUS:85046101321
T3 - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
SP - 1846
EP - 1851
BT - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
A2 - Yoo, Illhoi
A2 - Zheng, Jane Huiru
A2 - Gong, Yang
A2 - Hu, Xiaohua Tony
A2 - Shyu, Chi-Ren
A2 - Bromberg, Yana
A2 - Gao, Jean
A2 - Korkin, Dmitry
PB - Institute of Electrical and Electronics Engineers Inc.
Y2 - 13 November 2017 through 16 November 2017
ER -