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Database (Oxford). 2014 Oct 6;2014. pii: bau099. doi: 10.1093/database/bau099. Print 2014.

miRIAD-integrating microRNA inter- and intragenic data.

Author information

1
Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany pgalante@mochsl.org.br.
2
Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
3
Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil.
4
Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany.
5
Division of Medial Informatics, University of California San Diego, La Jolla, CA 93093-0505, USA.
6
Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil pgalante@mochsl.org.br christian.hinske@med.uni-muenchen.de.

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.

PMID:
25288656
PMCID:
PMC4186326
DOI:
10.1093/database/bau099
[Indexed for MEDLINE]
Free PMC Article

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