HMDD v2.0: a database for experimentally supported human microRNA and disease associations

The Human microRNA Disease Database (HMDD; available via the Web site at http://cmbi.bjmu.edu.cn/hmdd and http://202.38.126.151/hmdd/tools/hmdd2.html) is a collection of experimentally supported human microRNA (miRNA) and disease associations. Here, we describe the HMDD v2.0 update that presented several novel options for users to facilitate exploration of the data in the database. In the updated database, miRNA–disease association data were annotated in more details. For example, miRNA–disease association data from genetics, epigenetics, circulating miRNAs and miRNA–target interactions were integrated into the database. In addition, HMDD v2.0 presented more data that were generated based on concepts derived from the miRNA–disease association data, including disease spectrum width of miRNAs and miRNA spectrum width of human diseases. Moreover, we provided users a link to download all the data in the HMDD v2.0 and a link to submit novel data into the database. Meanwhile, we also maintained the old version of HMDD. By keeping data sets up-to-date, HMDD should continue to serve as a valuable resource for investigating the roles of miRNAs in human disease.

[1]  Yan Cui,et al.  SomamiR: a database for somatic mutations impacting microRNA function in cancer , 2012, Nucleic Acids Res..

[2]  Hui Zhou,et al.  ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data , 2012, Nucleic Acids Res..

[3]  Bing Shi,et al.  TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs , 2010, BMC Bioinformatics.

[4]  C. Croce,et al.  MicroRNA signatures in human cancers , 2006, Nature Reviews Cancer.

[5]  Hailin Chen,et al.  Similarity-based methods for potential human microRNA-disease association prediction , 2013, BMC Medical Genomics.

[6]  BarupalJitendra Kumar,et al.  ExcellmiRDB for translational genomics: a curated online resource for extracellular microRNAs. , 2015 .

[7]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[8]  H. Dweep,et al.  miRWalk2.0: a comprehensive atlas of microRNA-target interactions , 2015, Nature Methods.

[9]  Fabian J Theis,et al.  PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes , 2010, Genome Biology.

[10]  Reshmi Girijadevi,et al.  IntmiR: a complete catalogue of intronic miRNAs of human and mouse , 2011, Bioinformation.

[11]  Chi-Ying F. Huang,et al.  miRTarBase: a database curates experimentally validated microRNA–target interactions , 2010, Nucleic Acids Res..

[12]  Xing Chen,et al.  RWRMDA: predicting novel human microRNA-disease associations. , 2012, Molecular bioSystems.

[13]  S. Hammond.  MicroRNAs as tumor suppressors , 2007, Nature Genetics.

[14]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[15]  F. Slack,et al.  Oncomirs — microRNAs with a role in cancer , 2006, Nature Reviews Cancer.

[16]  Yadong Wang,et al.  miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..

[17]  Tongbin Li,et al.  miRecords: an integrated resource for microRNA–target interactions , 2008, Nucleic Acids Res..

[18]  Nectarios Koziris,et al.  TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support , 2011, Nucleic Acids Res..

[19]  Q. Cui,et al.  An Analysis of Human MicroRNA and Disease Associations , 2008, PloS one.

[20]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[21]  G. Calin,et al.  Clinical relevance of circulating cell-free microRNAs in cancer , 2014, Nature Reviews Clinical Oncology.

[22]  Gang Fu,et al.  Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data , 2014, Nucleic Acids Res..

[23]  Yan Cui,et al.  PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits , 2011, Nucleic Acids Res..

[24]  Xia Li,et al.  SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression , 2013, Bioinform..

[25]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[26]  V. Ambros.  The functions of animal microRNAs , 2004, Nature.

[27]  M. Latronico,et al.  Emerging role of microRNAs in cardiovascular biology. , 2007, Circulation research.

[28]  A. Tijsen,et al.  Circulating microRNAs: novel biomarkers and extracellular communicators in cardiovascular disease? , 2012, Circulation research.

[29]  Changning Liu,et al.  dbDEMC: a database of differentially expressed miRNAs in human cancers , 2010, BMC Genomics.

[30]  Hong-Mei Zhang,et al.  Genome‐wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis , 2012, Human mutation.

[31]  Dong Wang,et al.  Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases , 2010, Bioinform..

[32]  M. Esteller.  Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.

[33]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[34]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[35]  Qing Wu,et al.  miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes , 2011, Bioinform..

[36]  Andreas Kowarsch,et al.  PhenomiR: microRNAs in human diseases and biological processes. , 2012, Methods in molecular biology.

[37]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[38]  Geng Chen,et al.  Towards the understanding of microRNA and environmental factor interactions and their relationships to human diseases , 2012, Scientific Reports.

[39]  Ming Lu,et al.  TransmiR: a transcription factor–microRNA regulation database , 2009, Nucleic Acids Res..

[40]  Hsien-Da Huang,et al.  miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database , 2015, Nucleic Acids Res..