ToppMiR: Ranking MicroRNAs and Their MRNA Targets Based on Biological Functions and Context

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2014 May 16

PMID 24829448

Citations 11

Authors

Chao Wu

Eric E Bardes

Anil G Jegga

Bruce J Aronow

Affiliations

Soon will be listed here.

Abstract

Identifying functionally significant microRNAs (miRs) and their correspondingly most important messenger RNA targets (mRNAs) in specific biological contexts is a critical task to improve our understanding of molecular mechanisms underlying organismal development, physiology and disease. However, current miR-mRNA target prediction platforms rank miR targets based on estimated strength of physical interactions and lack the ability to rank interactants as a function of their potential to impact a given biological system. To address this, we have developed ToppMiR (http://toppmir.cchmc.org), a web-based analytical workbench that allows miRs and mRNAs to be co-analyzed via biologically centered approaches in which gene function associated annotations are used to train a machine learning-based analysis engine. ToppMiR learns about biological contexts based on gene associated information from expression data or from a user-specified set of genes that relate to context-relevant knowledge or hypotheses. Within the biological framework established by the genes in the training set, its associated information content is then used to calculate a features association matrix composed of biological functions, protein interactions and other features. This scoring matrix is then used to jointly rank both the test/candidate miRs and mRNAs. Results of these analyses are provided as downloadable tables or network file formats usable in Cytoscape.

Citing Articles

Integrated analysis using ToppMiR uncovers altered miRNA- mRNA regulatory networks in pediatric hepatocellular carcinoma-A pilot study.

Whyte S, Karns R, Min K, Cho J, Lee S, Lake C Cancer Rep (Hoboken). 2022; 6(1):e1685.

PMID: 35859536 PMC: 9875636. DOI: 10.1002/cnr2.1685.

Role of microRNA-25 in high glucose cultured Müller glia.

Liu Y, Shen H, Yuan S, Liu Q Int J Ophthalmol. 2021; 14(5):643-648.

PMID: 34012877 PMC: 8077003. DOI: 10.18240/ijo.2021.05.02.

MicroRNA-9-5p increases the sensitivity of colorectal cancer cells to 5-fluorouracil by downregulating high mobility group A2 expression.

Zheng H, Yan B, Wu Q, Zhang J Oncol Lett. 2021; 21(3):235.

PMID: 33613724 PMC: 7856691. DOI: 10.3892/ol.2021.12496.

LncRNA VPS9D1-AS1 promotes cell proliferation in acute lymphoblastic leukemia through modulating GPX1 expression by miR-491-5p and miR-214-3p evasion.

Xiao S, Xu N, Ding Q, Huang S, Zha Y, Zhu H Biosci Rep. 2020; 40(10).

PMID: 32808668 PMC: 7536331. DOI: 10.1042/BSR20193461.

MiR-26b regulates 5-FU-resistance in human colorectal cancer via down-regulation of Pgp.

Wang B, Lu F, Shi R, Feng Y, Zhao X, Lu Z Am J Cancer Res. 2019; 8(12):2518-2527.

PMID: 30662808 PMC: 6325481.

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