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ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context

Chao Wu, Eric E. Bardes, Anil G. Jegga, Bruce J. Aronow
2014 Nucleic Acids Research  
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  ...  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  ...  Prioritization of miRs by expression and biological functional relevance After the analysis and prioritization of mRNAs, ToppMiR ranks the miRs based on their putative regulations to their target mRNAs  ... 
doi:10.1093/nar/gku409 pmid:24829448 pmcid:PMC4086116 fatcat:xfiekqshmne4roqwleqep3bc6y

miTALOS v2: Analyzing Tissue Specific microRNA Function

Martin Preusse, Fabian J. Theis, Nikola S. Mueller, Bibekanand Mallick
2016 PLoS ONE  
MicroRNAs are involved in almost all biological processes and have emerged as regulators of signaling pathways.  ...  We incorporated the most recent and highest quality miRNA targeting data (TargetScan and StarBase), RNAseq based gene expression data (EBI Expression Atlas) and multiple new pathway data sources to increase  ...  Functional analysis of miRNAs depends on accurate identification of gene targets in a given biological context [2] .  ... 
doi:10.1371/journal.pone.0151771 pmid:26998997 pmcid:PMC4801359 fatcat:aou3asi6hjakbauoflllphwpwu

mirDIP 4.1—integrative database of human microRNA target predictions

Tomas Tokar, Chiara Pastrello, Andrea E M Rossos, Mark Abovsky, Anne-Christin Hauschild, Mike Tsay, Richard Lu, Igor Jurisica
2017 Nucleic Acids Research  
Even with modern high-throughput technologies, it is laborious and expensive to detect all possible microRNA targets.  ...  For this reason, several computational microRNA-target prediction tools have been developed, each with its own strengths and limitations.  ...  Ranks and associated precisions were log-transformed and their relationship was fitted by the quadratic function, imposing the rank as an independent variable.  ... 
doi:10.1093/nar/gkx1144 pmid:29194489 pmcid:PMC5753284 fatcat:4avz62zhafdvjen3c3tsgwtr3q

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

Shishan Xiao, Na Xu, Qian Ding, Shengwen Huang, Yan Zha, Hongqian Zhu
2020 Bioscience Reports  
Then, both miR-491-5p and miR-214-3p that was downregulated in ALL cells were affirmed to target GPX1.  ...  Functional assays further revealed that the proliferation was obstructed and the apoptosis was facilitated in ALL cells with silenced GPX1.  ...  ToppMiR: ranking microRNAs and their mRNA 463 targets based on biological functions and context. Nucleic Acids Res. Yu T, Wang LN, Li W, Zuo QF, Li MM, Zou QM, et al.  ... 
doi:10.1042/bsr20193461 pmid:32808668 pmcid:PMC7536331 fatcat:ro3in3q75nfhdpierxvvwevxx4