The microRNA.org resource: targets and expression

By Doron Betel, Manda Wilson, Aaron Gabow, Debora Marks, Christopher Sander. Nucleic Acids Res., 2007

2,602 citations recorded by the source corpus.

MicroRNA.org (http://www.microrna.org) is a comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. Using an improved graphical interface, a user can explore (i) the set of genes that are potentially regulated by a particular microRNA, (ii) the implied cooperativity of multiple microRNAs on a particular mRNA and (iii) microRNA expression profiles in various tissues. To facilitate future updates and development, the microRNA.org database structure and software architecture is flexibly designed to incorporate new expression and target discoveries. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5568473bd3ef0a2a172152fa9eb5df6a79066ded

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Citations in the corpus

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Targeting MicroRNAs in Cancer: Rationale, Strategies and Challenges (2010, neutral): “Each miRNA has the potential to target a large number of genes (on average about 500 for each miRNA family”
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse (2015, background): “miRanda (30), TargetScan (38), PicTar (34), MicroCosm (28) and micorT (29), are included.”
miRTarBase: a database curates experimentally validated microRNA–target interactions (2010, neutral): “Additionally, among the several computational methods and web-based programs developed to identify target genes of miRNAs include miRanda (6), TargetScan (13), RNAhybrid (14), Pictar (15) and PITA (16).”
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Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse (2018, neutral): “Furthermore, information about regulatory motifs, micro-RNA predictions (microRNA binding [31], microRNA targets [32]) and chromatin state predictions (ChromHMM [33]) were taken into account.”
Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency (2011, methodology): “miR302/367 collectively targets hundreds of different mRNA targets, including those that regulate chromatin remodeling and cell proliferation based on bioinformatic prediction algorithms (Betel et al., 2008; Grimson et al., 2007; Krek et al., 2005).”
miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets (2012, methodology): “Seven algorithms predicting miRNA targets, DIANA-microT [13,14], miRanda [9,22,23], mirBridge [15], PicTar [16], PITA [18] , rna22 [17] , and TargetScan [10,11,12], and two experimentally validated databases, TarBase [24] and miRecords [25], of miRNA target genes were included.”
miR2Disease: a manually curated database for microRNA deregulation in human disease (2008, neutral): “org (14) collect experimentally validated”
Desperately seeking microRNA targets (2010, background): “Seed pairing is weighed more strongly than pairing elsewher”
Tools for Sequence-Based miRNA Target Prediction: What to Choose? (2016, methodology): “As a result of a target mRNA search, the complete gene sequence, the target sites of each miRNA and the miRNA:mRNA interactions are displayed as sorted by the mirSVR score and PhastCons score (see Table 2) [64,91].”
MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review (2012, neutral): “Considering the different rules regulating the interaction between a microRNA and its target mRNA, it is not surprising that each miRNA has the potential to target a large number of genes (Betel et al, 2008; Friedman et al, 2009; Krek et al, 2005; Lewis et al, 2005).”
miRBase: integrating microRNA annotation and deep-sequencing data (2010, background): “org (22)], together with lists of validated microRNA target sites [currently curated by resources such as TarBase (23), miRecords (24), miRTarBase].”
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