PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways
Open Access
- 24 October 2013
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 42 (D1), D86-D91
- https://doi.org/10.1093/nar/gkt1028
Abstract
Polymorphisms in microRNAs (miRNAs) and their target sites (PolymiRTS) are known to disrupt miRNA function, leading to the development of disease and variation in physiological and behavioral phenotypes. Here, we describe recent updates to the PolymiRTS database (http://compbio.uthsc.edu/miRSNP), an integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. Recent advances in genomic technologies have made it possible to identify miRNA–mRNA binding sites from direct mapping experiments such as CLASH (cross linking, ligation and sequencing of hybrids). We have integrated data from CLASH experiments in the PolymiRTS database to provide more complete and accurate miRNA–mRNA interactions. Other significant new features include (i) small insertions and deletions in miRNA seed regions and miRNA target sites, (ii) TargetScan context + score differences for assessing the impact of polymorphic miRNA–mRNA interactions and (iii) biological pathways. The browse and search pages of PolymiRTS allow users to explore the relations between the PolymiRTSs and gene expression traits, physiological and behavioral phenotypes, human diseases and biological pathways.Keywords
This publication has 49 references indexed in Scilit:
- Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical BindingCell, 2013
- MicroRNAs in Alzheimer's diseaseNeurobiology of Disease, 2012
- MicroRNAs in Stress Signaling and Human DiseaseCell, 2012
- BioMart Central Portal: an open database network for the biological communityDatabase: The Journal of Biological Databases and Curation, 2011
- Potential etiologic and functional implications of genome-wide association loci for human diseases and traitsProceedings of the National Academy of Sciences of the United States of America, 2009
- miRecords: an integrated resource for microRNA-target interactionsNucleic Acids Research, 2008
- The NCBI dbGaP database of genotypes and phenotypesNature Genetics, 2007
- Human polymorphism at microRNAs and microRNA target sitesProceedings of the National Academy of Sciences of the United States of America, 2007
- WebQTL: Web-Based Complex Trait AnalysisNeuroinformatics, 2003
- dbSNP: the NCBI database of genetic variationNucleic Acids Research, 2001