Dataset Information

MiRIAD-integrating microRNA inter- and intragenic data.

ABSTRACT: MicroRNAs (miRNAs) are a class of small (?22 nucleotides) non-coding RNAs that post-transcriptionally regulate gene expression by interacting with target mRNAs. A majority of miRNAs is located within intronic or exonic regions of protein-coding genes (host genes), and increasing evidence suggests a functional relationship between these miRNAs and their host genes. Here, we introduce miRIAD, a web-service to facilitate the analysis of genomic and structural features of intragenic miRNAs and their host genes for five species (human, rhesus monkey, mouse, chicken and opossum). miRIAD contains the genomic classification of all miRNAs (inter- and intragenic), as well as classification of all protein-coding genes into host or non-host genes (depending on whether they contain an intragenic miRNA or not). We collected and processed public data from several sources to provide a clear visualization of relevant knowledge related to intragenic miRNAs, such as host gene function, genomic context, names of and references to intragenic miRNAs, miRNA binding sites, clusters of intragenic miRNAs, miRNA and host gene expression across different tissues and expression correlation for intragenic miRNAs and their host genes. Protein-protein interaction data are also presented for functional network analysis of host genes. In summary, miRIAD was designed to help the research community to explore, in a user-friendly environment, intragenic miRNAs, their host genes and functional annotations with minimal effort, facilitating hypothesis generation and in-silico validations. Database URL: http://www.miriad-database.org.

SUBMITTER: Hinske LC

PROVIDER: S-EPMC4186326 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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miRIAD-integrating microRNA inter- and intragenic data.

Hinske Ludwig Christian LC França Gustavo S GS Torres Hugo A M HA Ohara Daniel T DT Lopes-Ramos Camila M CM Heyn Jens J Reis Luiz F L LF Ohno-Machado Lucila L Kreth Simone S Galante Pedro A F PA

Database : the journal of biological databases and curation 20141006

MicroRNAs (miRNAs) are a class of small (∼22 nucleotides) non-coding RNAs that post-transcriptionally regulate gene expression by interacting with target mRNAs. A majority of miRNAs is located within intronic or exonic regions of protein-coding genes (host genes), and increasing evidence suggests a functional relationship between these miRNAs and their host genes. Here, we introduce miRIAD, a web-service to facilitate the analysis of genomic and structural features of intragenic miRNAs and their ...[more]

PMID: 25288656

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Project description:BackgroundToday's species names are entry points into a web of publicly available knowledge and are integral parts of legislation concerning biological conservation and consumer safety. Species information usually is fragmented, can be misleading due to the existence of different names and might even be biased because of an identical name that is used for a different species. Safely navigating through the name space is one of the most challenging tasks when associating names with data and when decisions are made which name to include in legislation. Integrating publicly available dynamic data to characterise plant genetic resources of botanic gardens and other facilities will significantly increase the efficiency of recovering relevant information for research projects, identifying potentially invasive taxa, constructing priority lists and developing DNA-based specimen authentication.New informationTo demonstrate information availability and discuss integration into botanic collections, scientific names derived from botanic gardens were evaluated using the Encyclopedia of Life, The Catalogue of Life and The Plant List. 98.5% of the names could be verified by the combined use of these providers. Comparing taxonomic status information 13 % of the cases were in disagreement. About 7 % of the verified names were found to be included in the International Union for Conservation of Nature Red List, including one extinct taxon and three taxa with the status "extinct in the wild". As second most important factor for biodiversity loss, potential invasiveness was determined. Approximately 4 % of the verified names were detected using the Global Invasive Species Information Network, including 208 invasive taxa. According to Delivering Alien Invasive Species Inventories for Europe around 20 % of the verified names are European alien taxa including 15 of the worst European invasive taxa. Considering alternative names in the data recovery process, success increased up to 18 %.

Dataset Information

MiRIAD-integrating microRNA inter- and intragenic data.

Publications

miRIAD-integrating microRNA inter- and intragenic data.

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