by Christoph on January 25, 2012
Single nucleotide polymorphisms (SNPs) can lead to the susceptibility and onset of diseases through their effects on gene expression at the posttranscriptional level. Recent findings indicate that SNPs could create, destroy, or modify the efficiency of miRNA binding to the 3′UTR of a gene, resulting in gene dysregulation. With the rapidly growing number of published disease-associated SNPs (dSNPs), there is a strong need for resources specifically recording dSNPs on the 3′UTRs and their nucleotide distance from miRNA target sites. Bruno et al. from the Center for Computational Research SUNY at the University of Buffalo presents miRdSNP, a database incorporating three important areas of dSNPs, miRNA target sites, and diseases.
miRdSNP provides a unique database of dSNPs on the 3′UTRs of human genes manually curated from PubMed. The current release includes 786 dSNP-disease associations for 630 unique dSNPs and 204 disease types. miRdSNP annotates genes with experimentally confirmed targeting by miRNAs and indexes miRNA target sites predicted by TargetScan and PicTar as well as potential miRNA target sites newly generated by dSNPs. A robust web interface and search tools are provided for [click to continue…]
Incoming search terms for this article:
by Christoph on December 8, 2011
Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs.
Izabela Makałowska’s Laboratory of Evolutionary Genomics at The Adam Mickiewicz University in Poznan just published miRNEST, a comprehensive database of animal, plant and virus microRNAs. The core part of the database is built from the author’s miRNA predictions conducted on Expressed Sequence Tags of 225 animal and 202 plant species. The miRNA search was performed based on sequence similarity and as many as 10 004 miRNA candidates in 221 animal and 199 plant species were discovered. Out of them only 299 have already been deposited in miRBase. Additionally, miRNEST has been integrated with external miRNA data from literature and 13 databases, which includes miRNA sequences, small RNA sequencing data, expression, polymorphisms and targets data as well as links to external miRNA resources, whenever applicable. All this makes miRNEST a considerable miRNA resource in a sense of number of species (544) that integrates a scattered miRNA data into a uniform format with a user-friendly web interface.
miRNEST: http://mirnest.amu.edu.pl
Michal Wojciech Szczesniak, Sebastian Deorowicz, Jakub Gapski, Lukasz Kaczynski, and Izabela Makalowska
miRNEST database: an integrative approach in microRNA search and annotation
Nucleic Acids Res. 2011
http://nar.oxfordjournals.org/content/early/2011/11/30/nar.gkr1159
Incoming search terms for this article:
by Christoph on October 19, 2011
The regulatory role of microRNAs (miRNAs) has been well studied in a wide variety of biological processes but there have been litle systematic efforts to understand and analyze the genetic variations in miRNA loci and study its functional consequences.
Vinod Scaria’s group at the Institute of Genomics and Integrative Biology (CSIR) in Delhi comprehensively curated genetic variations in miRNA loci in the human genome and established a computational pipeline to assess potential functional consequences of these variants along with methods for systematic curation and reporting of variations in these loci. The resulting database miRvar is a community curation resource, a starting point for systematic curation and analysis of genetic variants in miRNA loci.
The data is made available on the Leiden Open (source) Variation Database (LOVD) platform at http://genome.igib.res.in/mirlovd to provide ease of aggregation and analysis. It is open for community curation efforts. miRvar allows to search variants in different miRNAs and has information about the variant position and the allele change in the respective miRNA, in addition to making it easy to browse for information through linkouts like miRBase, UCSC Genome Browser, miR2Disease, 1000 Genomes Project and miRecords. Currently, the database comprises of a total 108 unique entries including 85 miRNAs from UCSC-dbSNP mapping and 25 from published literature. The database also allows to search for miRNAs using their names, disease associations, location of SNP on the hairpin structure and chromosome.
Bhartiya, D., Laddha, S. V., Mukhopadhyay, A. and Scaria, V. (2011),
miRvar: A comprehensive database for genomic variations in microRNAs.
Human Mutation, 32: E2226–E2245.
http://onlinelibrary.wiley.com/doi/10.1002/humu.21482/abstract
Incoming search terms for this article:
by Christoph on October 30, 2009
Thanks go to our reader Qinghua Jiang who pointed out a data base called miR2Disease. This collaboration project between the Harbin Institute of Technology (HIT) and the Center of Computational Biology and Bioinformatics at the Indiana University of Medical School is a manually curated microRNA-disease database focusing on miRNA deregulation in various human diseases.
The current version (latest update Sep09) of miR2Disease documents 2663 curated relationships between 347 human microRNAs and 127 human diseases. In the initial release in Jan09 around one-seventh of the microRNA–disease relationships represented the pathogenic roles of deregulated microRNA in human disease. Each entry in the miR2Disease contains detailed information on a microRNA–disease relationship, including a microRNA ID, the disease name, a brief description of the microRNA–disease relationship, an expression pattern of the microRNA, the detection method for microRNA expression, experimentally verified target gene(s) of the microRNA and a literature reference. miR2Disease allows to search by microRNA ID, disease name, or target gene. In addition, miR2Disease offers a submission page that allows researchers to submit established microRNA–disease relationships that are not documented. Once approved by the submission review committee, the submitted records will be included in the database.
The miR2Disease database is available at: http://www.miR2Disease.org/
- Jiang Q., Wang Y., Hao Y., Juan L., Teng M., Zhang X., Li M., Wang G., Liu Y., (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37:D98-104.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686559/
Incoming search terms for this article:
by Chris on September 21, 2009
miRò is a web-based knowledge base that provides users with miRNA–phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities. The main goal of miRò is the establishment of a knowledge base which allows non-trivial analysis through sophisticated mining techniques and the introduction of a new layer of associations between genes and phenotypes inferred based on miRNAs annotations. Furthermore, a specificity function applied to validated data highlights the most significant associations.
The miRò web site is available at: http://ferrolab.dmi.unict.it/miro.
Incoming search terms for this article:
Loading ...
