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The microRNA.org resource: targets and expression.

Betel D, Wilson M, Gabow A, Marks DS, Sander C - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, NY, USA.

ABSTRACT
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.

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Related in: MedlinePlus

Scientific use cases for exploring microRNA target predictions. In case A, users search for the ‘predicted target genes of a given microRNA’. In the gene list view, an expandable display shows a schematic view of the microRNA target sites on a selected target gene. A selected target gene is also hyperlinked to a detailed view of the microRNA-binding sites in the 3′-UTR, including exact nucleotide positions, microRNA:mRNA duplex, alignment score and conservation as well as the ranked list of the binding sites. Similarly, in case B, users can reach the detailed target-sites-on-sequence view by ‘querying by gene name’.
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Figure 1: Scientific use cases for exploring microRNA target predictions. In case A, users search for the ‘predicted target genes of a given microRNA’. In the gene list view, an expandable display shows a schematic view of the microRNA target sites on a selected target gene. A selected target gene is also hyperlinked to a detailed view of the microRNA-binding sites in the 3′-UTR, including exact nucleotide positions, microRNA:mRNA duplex, alignment score and conservation as well as the ranked list of the binding sites. Similarly, in case B, users can reach the detailed target-sites-on-sequence view by ‘querying by gene name’.

Mentions: Scientific use case scenarios


The microRNA.org resource: targets and expression.

Betel D, Wilson M, Gabow A, Marks DS, Sander C - Nucleic Acids Res. (2007)

Scientific use cases for exploring microRNA target predictions. In case A, users search for the ‘predicted target genes of a given microRNA’. In the gene list view, an expandable display shows a schematic view of the microRNA target sites on a selected target gene. A selected target gene is also hyperlinked to a detailed view of the microRNA-binding sites in the 3′-UTR, including exact nucleotide positions, microRNA:mRNA duplex, alignment score and conservation as well as the ranked list of the binding sites. Similarly, in case B, users can reach the detailed target-sites-on-sequence view by ‘querying by gene name’.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238905&req=5

Figure 1: Scientific use cases for exploring microRNA target predictions. In case A, users search for the ‘predicted target genes of a given microRNA’. In the gene list view, an expandable display shows a schematic view of the microRNA target sites on a selected target gene. A selected target gene is also hyperlinked to a detailed view of the microRNA-binding sites in the 3′-UTR, including exact nucleotide positions, microRNA:mRNA duplex, alignment score and conservation as well as the ranked list of the binding sites. Similarly, in case B, users can reach the detailed target-sites-on-sequence view by ‘querying by gene name’.
Mentions: Scientific use case scenarios

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Computational and Systems Biology Center, Memorial Sloan-Kettering Cancer Center, NY, USA.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus