miRWalk - Database: Prediction of possible miRNA binding sites by walking the genes of three genomes
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TLDR
The miRWalk database as mentioned in this paper is a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat.About:
This article is published in Journal of Biomedical Informatics.The article was published on 2011-10-01 and is currently open access. It has received 1603 citations till now. The article focuses on the topics: MiRNA binding & Untranslated region.read more
Citations
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MicroRNA-181b inhibits glycolysis in gastric cancer cells via targeting hexokinase 2 gene
TL;DR: It is reported that miR-181b negatively regulates glycolysis in gastric cancer cells and represses cell proliferation and migration and is dramatically down-regulated in human gastric cancers.
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MicroRNA Regulates Hepatocytic Differentiation of Progenitor Cells by Targeting YAP1.
Kwang Hwa Jung,Ryan L. McCarthy,Chong Zhou,Nadima Uprety,Michelle Craig Barton,Laura Beretta +5 more
TL;DR: In this article, microRNA expression profiling in human liver progenitor cells following hepatocytic differentiation identified miR122 and miR-194 as the microRNAs most strongly upregulated during hepatocytosis.
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Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
Lingfei Wang,Tom Michoel +1 more
TL;DR: A novel method and ultra-fast software Findr is developed for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations.
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Improving miRNA-mRNA interaction predictions
Daniel Tabas-Madrid,Ander Muniategui,Ignacio Sánchez-Caballero,Dannys Jorge Martinez-Herrera,Carlos Oscar S. Sorzano,Angel Rubio,Alberto Pascual-Montano +6 more
TL;DR: Two methods to measure the confidence of predicted interactions based on experimentally validated information are proposed and reduce the selection of interactions to a unique database based on an intuitive score and allow comparing databases between them.
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Macros in microRNA target identification: A comparative analysis of in silico, in vitro, and in vivo approaches to microRNA target identification
Shikha Tarang,Michael D. Weston +1 more
TL;DR: The present review summarizes the important features of each of the experimental approaches, their technical and biological limitations, and future challenges in light of the complexity of miRNA target gene recognition.
References
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MicroRNAs: Genomics, Biogenesis, Mechanism, and Function
TL;DR: Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
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The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
TL;DR: Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin- 4 regulates lin- 14 translation via an antisense RNA-RNA interaction.
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Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
TL;DR: In a four-genome analysis of 3' UTRs, approximately 13,000 regulatory relationships were detected above the estimate of false-positive predictions, thereby implicating as miRNA targets more than 5300 human genes, which represented 30% of the gene set.
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MicroRNA expression profiles classify human cancers
Jun Lu,Gad Getz,Eric A. Miska,Eric A. Miska,Ezequiel Alvarez-Saavedra,Justin Lamb,David Peck,Alejandro Sweet-Cordero,Alejandro Sweet-Cordero,Benjamin L. Ebert,Benjamin L. Ebert,Raymond H. Mak,Raymond H. Mak,Adolfo A. Ferrando,James R. Downing,Tyler Jacks,H. Robert Horvitz,H. Robert Horvitz,Todd R. Golub,Todd R. Golub,Todd R. Golub +20 more
TL;DR: A new, bead-based flow cytometric miRNA expression profiling method is used to present a systematic expression analysis of 217 mammalian miRNAs from 334 samples, including multiple human cancers, and finds the miRNA profiles are surprisingly informative, reflecting the developmental lineage and differentiation state of the tumours.
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Prediction of Mammalian MicroRNA Targets
TL;DR: The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions.