title: 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.
authors.affiliation: Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany pgalante@mochsl.org.br.
authors.forename: Ludwig Christian
authors.initials: LC
authors.lastname: Hinske
authors.affiliation: 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.
authors.forename: Gustavo S
authors.initials: GS
authors.lastname: França
authors.affiliation: Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil.
authors.forename: Hugo A M
authors.initials: HA
authors.lastname: Torres
authors.affiliation: Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil.
authors.forename: Daniel T
authors.initials: DT
authors.lastname: Ohara
authors.affiliation: Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil.
authors.forename: Camila M
authors.initials: CM
authors.lastname: Lopes-Ramos
authors.affiliation: Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Heyn
authors.affiliation: Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil.
authors.forename: Luiz F L
authors.initials: LF
authors.lastname: Reis
authors.affiliation: Division of Medial Informatics, University of California San Diego, La Jolla, CA 93093-0505, USA.
authors.forename: Lucila
authors.initials: L
authors.lastname: Ohno-Machado
authors.affiliation: Clinic of Anaesthesiology, Clinic of the University of Munich, Munich, Germany.
authors.forename: Simone
authors.initials: S
authors.lastname: Kreth
authors.affiliation: Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil pgalante@mochsl.org.br christian.hinske@med.uni-muenchen.de.
authors.forename: Pedro A F
authors.initials: PA
authors.lastname: Galante
mesh_terms: D000818:Animals; D002645:Chickens; D021901:DNA, Intergenic / Q000235:genetics*; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D008253:Macaca mulatta; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D009893:Opossums; D012984:Software
chemical_list: D021901:DNA, Intergenic; D035683:MicroRNAs