SURVEY AND SUMMARY Bioinformatic tools for microRNA dissection

Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks. MiRNAs are endogenous single-stranded non-coding RNAs (∼22-nt long) that regulate gene expression at the post-transcriptional level. Through pairing with mRNA, miRNAs can down-regulate gene expression by inhibiting translation or stimulating mRNA degradation. In some cases they can also up-regulate the expression of a target gene. MiRNAs influence a variety of cellular pathways that range from development to carcinogenesis. The involvement of miRNAs in several human diseases, particularly cancer, makes them potential diagnostic and prognostic biomarkers. Recent technological advances, especially highthroughput sequencing, have led to an exponential growth in the generation of miRNA-related data. A number of bioinformatic tools and databases have been devised to manage this growing body of data. We analyze 129 miRNA tools that are being used in diverse areas of miRNA research, to assist investigators in choosing the most appropriate tools for their needs.

[1]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[2]  M. Khoury,et al.  The Human Genome Epidemiology Network. , 1998, American journal of epidemiology.

[3]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[4]  B. Reinhart,et al.  The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans , 2000, Nature.

[5]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[6]  A. Pasquinelli,et al.  A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA , 2001, Science.

[7]  V. Ambros.  microRNAs Tiny Regulators with Great Potential , 2001, Cell.

[8]  C. Croce,et al.  Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  G. Rubin,et al.  Computational identification of Drosophila microRNA genes , 2003, Genome Biology.

[10]  C. Burge,et al.  The microRNAs of Caenorhabditis elegans. , 2003, Genes & development.

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

[12]  J. Wengel,et al.  LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. , 2004, Biochemistry.

[13]  K. Czaplinski,et al.  Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. , 2004, RNA.

[14]  Sanghyuk Lee,et al.  MicroRNA genes are transcribed by RNA polymerase II , 2004, The EMBO journal.

[15]  R. Giegerich,et al.  Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.

[16]  Y. Yatabe,et al.  Reduced Expression of the let-7 MicroRNAs in Human Lung Cancers in Association with Shortened Postoperative Survival , 2004, Cancer Research.

[17]  B. Cullen,et al.  Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. , 2004, RNA.

[18]  A. Bradley,et al.  Identification of mammalian microRNA host genes and transcription units. , 2004, Genome research.

[19]  Anton J. Enright,et al.  Identification of Virus-Encoded MicroRNAs , 2004, Science.

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

[21]  C. Croce,et al.  An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  B. Cullen,et al.  Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. , 2004, Nucleic acids research.

[23]  Byoung-Tak Zhang,et al.  Human microRNA prediction through a probabilistic co-learning model of sequence and structure , 2005, Nucleic acids research.

[24]  M. Daly,et al.  Genome-wide association studies for common diseases and complex traits , 2005, Nature Reviews Genetics.

[25]  B. Bartel.  MicroRNAs directing siRNA biogenesis , 2005, Nature Structural &Molecular Biology.

[26]  R. Russell,et al.  Principles of MicroRNA–Target Recognition , 2005, PLoS biology.

[27]  Chang-Zheng Chen,et al.  MicroRNAs as oncogenes and tumor suppressors. , 2005, The New England journal of medicine.

[28]  R. Pillai.  MicroRNA function: multiple mechanisms for a tiny RNA? , 2005, RNA.

[29]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[30]  C. Croce,et al.  MicroRNAs 221 and 222 inhibit normal erythropoiesis and erythroleukemic cell growth via kit receptor down-modulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[31]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[32]  C. Burge,et al.  The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution , 2005, Science.

[33]  De-Pei Liu,et al.  The role of small RNAs in human diseases: Potential troublemaker and therapeutic tools , 2005, Medicinal research reviews.

[34]  Yuanji Zhang,et al.  miRU: an automated plant miRNA target prediction server , 2005, Nucleic Acids Res..

[35]  V. Kim.  MicroRNA biogenesis: coordinated cropping and dicing , 2005, Nature Reviews Molecular Cell Biology.

[36]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[37]  Hsien-Da Huang,et al.  miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes , 2005, Nucleic Acids Res..

[38]  Todd A. Anderson,et al.  Computational identification of microRNAs and their targets , 2006, Comput. Biol. Chem..

[39]  B. Davidson,et al.  RNA polymerase III transcribes human microRNAs , 2006, Nature Structural &Molecular Biology.

[40]  Mihaela Zavolan,et al.  Inference of miRNA targets using evolutionary conservation and pathway analysis , 2007, BMC Bioinformatics.

[41]  Q. Cui,et al.  Principles of microRNA regulation of a human cellular signaling network , 2006, Molecular systems biology.

[42]  C. Ya.  MicroRNA and Cancer , 2006 .

[43]  Jan Krüger,et al.  RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..

[44]  Yvonne Tay,et al.  A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes , 2006, Cell.

[45]  Louise C. Showe,et al.  Bioinformatics Original Paper Combining Multi-species Genomic Data for Microrna Identification Using a Naı¨ve Bayes Classifier , 2022 .

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

[47]  Byoung-Tak Zhang,et al.  ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs , 2006, Nucleic Acids Res..

[48]  N. Rajewsky.  microRNA target predictions in animals , 2006, Nature Genetics.

[49]  R. Plasterk,et al.  RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. , 2005, RNA.

[50]  Colin N. Dewey,et al.  A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans , 2006, Current Biology.

[51]  Bin Fan,et al.  MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans , 2007, BMC Bioinformatics.

[52]  Hsien-Da Huang,et al.  ViTa: prediction of host microRNAs targets on viruses , 2006, Nucleic Acids Res..

[53]  É. Várallyay,et al.  Detection of microRNAs by Northern blot analyses using LNA probes. , 2007, Methods.

[54]  R. Weinberg,et al.  Tumour invasion and metastasis initiated by microRNA-10b in breast cancer , 2007, Nature.

[55]  A. O. Chiromatzo,et al.  miRNApath: a database of miRNAs, target genes and metabolic pathways. , 2007, Genetics and molecular research : GMR.

[56]  B. Lenhard,et al.  Mammalian MicroRNA Prediction through a Support Vector Machine Model of Sequence and Structure , 2007, PloS one.

[57]  Louise C. Showe,et al.  Naïve Bayes for microRNA target predictions - machine learning for microRNA targets , 2007, Bioinform..

[58]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[59]  Anton J. Enright,et al.  Prediction of microRNA targets. , 2007, Drug discovery today.

[60]  D. Banerjee,et al.  A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance , 2007, Proceedings of the National Academy of Sciences.

[61]  J. Steitz,et al.  Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation , 2007, Science.

[62]  Taishin Kin,et al.  miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. , 2007, RNA.

[63]  A. Schier,et al.  Target Protectors Reveal Dampening and Balancing of Nodal Agonist and Antagonist by miR-430 , 2007, Science.

[64]  Margaret S. Ebert,et al.  MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells , 2007, Nature Methods.

[65]  P. Sætrom,et al.  MicroRNA-directed transcriptional gene silencing in mammalian cells , 2008, Proceedings of the National Academy of Sciences.

[66]  W. Gerald,et al.  Endogenous human microRNAs that suppress breast cancer metastasis , 2008, Nature.

[67]  E. Wang,et al.  MicroRNA Regulatory Patterns on the Human Metabolic Network~!2008-10-09~!2008-10-22~!2008-11-28~! , 2008 .

[68]  Wen-chang Lin,et al.  Vir-Mir db: prediction of viral microRNA candidate hairpins , 2007, Nucleic Acids Res..

[69]  Xiaowei Wang.  miRDB: a microRNA target prediction and functional annotation database with a wiki interface. , 2008, RNA.

[70]  A. Harris,et al.  Detection of elevated levels of tumour‐associated microRNAs in serum of patients with diffuse large B‐cell lymphoma , 2008, British journal of haematology.

[71]  N. Rajewsky,et al.  Discovering microRNAs from deep sequencing data using miRDeep , 2008, Nature Biotechnology.

[72]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[73]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[74]  W. L. Ruzzo,et al.  MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries , 2008, Stem cells.

[75]  W. Rottbauer,et al.  MicroRNA-21 contributes to myocardial disease by stimulating MAP kinase signalling in fibroblasts , 2008, Nature.

[76]  Qihong Huang,et al.  Small-molecule inhibitors of microrna miR-21 function. , 2008, Angewandte Chemie.

[77]  D. Zack,et al.  Analysis of regulatory network topology reveals functionally distinct classes of microRNAs , 2008, Nucleic acids research.

[78]  Yi-Hsuan Chen,et al.  miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes , 2007, Nucleic Acids Res..

[79]  Angela Re,et al.  CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse , 2010, BMC Bioinformatics.

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

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

[82]  R. Gregory,et al.  Many roads to maturity: microRNA biogenesis pathways and their regulation , 2009, Nature Cell Biology.

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

[84]  Albertha J. M. Walhout,et al.  The interplay between transcription factors and microRNAs in genome‐scale regulatory networks , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.

[85]  Martin Reczko,et al.  DIANA-mirPath: Integrating human and mouse microRNAs in pathways , 2009, Bioinform..

[86]  P. Poirazi,et al.  Prediction of novel microRNA genes in cancer-associated genomic regions—a combined computational and experimental approach , 2009, Nucleic acids research.

[87]  Li Li,et al.  Computational approaches for microRNA studies: a review , 2010, Mammalian Genome.

[88]  A. T. Freitas,et al.  Current tools for the identification of miRNA genes and their targets , 2009, Nucleic acids research.

[89]  Michal Ziv-Ukelson,et al.  Gene bi-targeting by viral and human miRNAs , 2010, BMC Bioinformatics.

[90]  Dennis Shasha,et al.  miRò: a miRNA knowledge base , 2009, Database J. Biol. Databases Curation.

[91]  Sanghamitra Bandyopadhyay,et al.  PuTmiR: A database for extracting neighboring transcription factors of human microRNAs , 2010, BMC Bioinformatics.

[92]  Panayiotis V. Benos,et al.  HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models , 2009, BMC Bioinformatics.

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

[94]  S. Lowe,et al.  miR-221 overexpression contributes to liver tumorigenesis , 2009, Proceedings of the National Academy of Sciences.

[95]  T. Sandström,et al.  Adverse cardiovascular effects of air pollution , 2009, Nature Clinical Practice Cardiovascular Medicine.

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

[97]  Ana M. Aransay,et al.  miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments , 2009, Nucleic Acids Res..

[98]  Nectarios Koziris,et al.  DIANA-microT web server: elucidating microRNA functions through target prediction , 2009, Nucleic Acids Res..

[99]  John P. A. Ioannidis,et al.  Human Genome Epidemiology , 2009 .

[100]  W. Cho.  MicroRNAs: potential biomarkers for cancer diagnosis, prognosis and targets for therapy. , 2010, The international journal of biochemistry & cell biology.

[101]  C. Harris,et al.  Genetic variation in microRNA networks: the implications for cancer research , 2010, Nature Reviews Cancer.

[102]  Hsien-Da Huang,et al.  miRTar: an integrated system for identifying miRNA-target interactions in human , 2011, BMC Bioinformatics.

[103]  Pascal Barbry,et al.  Bioinformatics Applications Note Gene Expression Mirontop: Mining Micrornas Targets across Large Scale Gene Expression Studies , 2022 .

[104]  P. Poirazi,et al.  MatureBayes: A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors , 2010, PloS one.

[105]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[106]  C. Croce,et al.  Targeting microRNAs in cancer: rationale, strategies and challenges , 2010, Nature Reviews Drug Discovery.

[107]  Jason Weston,et al.  A user's guide to support vector machines. , 2010, Methods in molecular biology.

[108]  D. Weinberger,et al.  MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets , 2010, Human mutation.

[109]  Yong Huang,et al.  The discovery approaches and detection methods of microRNAs , 2011, Molecular Biology Reports.

[110]  Michel Georges,et al.  Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates , 2008, Nucleic Acids Res..

[111]  C. Sonnenschein,et al.  Environmental causes of cancer: endocrine disruptors as carcinogens , 2010, Nature Reviews Endocrinology.

[112]  M. Siomi,et al.  Posttranscriptional regulation of microRNA biogenesis in animals. , 2010, Molecular cell.

[113]  M. Caligiuri,et al.  miR-328 Functions as an RNA Decoy to Modulate hnRNP E2 Regulation of mRNA Translation in Leukemic Blasts , 2010, Cell.

[114]  Gabriele Sales,et al.  MAGIA, a web-based tool for miRNA and Genes Integrated Analysis , 2010, Nucleic Acids Res..

[115]  Anjali J. Koppal,et al.  Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites , 2010, Genome Biology.

[116]  Xuan Pan,et al.  MicroRNA-21: A novel therapeutic target in human cancer , 2010, Cancer biology & therapy.

[117]  Fons J. Verbeek,et al.  Comparison and Integration of Target Prediction Algorithms for microRNA Studies , 2010, J. Integr. Bioinform..

[118]  A. Hatzigeorgiou,et al.  The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function , 2010, PloS one.

[119]  Ashwin Srinivasan,et al.  Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM) , 2010, BMC Bioinformatics.

[120]  David J. Arenillas,et al.  MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model , 2011, BMC Bioinformatics.

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

[122]  Michal Linial,et al.  MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets , 2010, Bioinform..

[123]  Hui Zhou,et al.  starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data , 2010, Nucleic Acids Res..

[124]  C. Bracken,et al.  Experimental strategies for microRNA target identification , 2011, Nucleic acids research.

[125]  A. Bader,et al.  Developing therapeutic microRNAs for cancer , 2011, Gene Therapy.

[126]  Ana M. Aransay,et al.  miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments , 2011, Nucleic Acids Res..

[127]  Nectarios Koziris,et al.  DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association , 2011, Nucleic Acids Res..

[128]  Hanah Margalit,et al.  RepTar: a database of predicted cellular targets of host and viral miRNAs , 2010, Nucleic Acids Res..

[129]  Aybar C. Acar,et al.  mESAdb: microRNA Expression and Sequence Analysis Database , 2010, Nucleic Acids Res..

[130]  Andrew E. Bruno,et al.  miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes , 2012, BMC Genomics.

[131]  Fabian J Theis,et al.  miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. , 2011, RNA.

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

[133]  M. Nykter,et al.  Circulating Plasma MiR-141 Is a Novel Biomarker for Metastatic Colon Cancer and Predicts Poor Prognosis , 2011, PloS one.

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

[135]  Wei Wu.  MicroRNA and Cancer , 2011, Methods in Molecular Biology.

[136]  I. Jurisica,et al.  NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs , 2011, PloS one.

[137]  Panayiotis V. Benos,et al.  mirConnX: condition-specific mRNA-microRNA network integrator , 2011, Nucleic Acids Res..

[138]  R. Regazzi,et al.  Diabetes mellitus, a microRNA-related disease? , 2011, Translational research : the journal of laboratory and clinical medicine.

[139]  H. Haller,et al.  MicroRNAs as mediators and therapeutic targets in chronic kidney disease , 2011, Nature Reviews Nephrology.

[140]  Laurent F. Thomas,et al.  Inferring causative variants in microRNA target sites , 2011, Nucleic acids research.

[141]  Norbert Gretz,et al.  miRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes , 2011, J. Biomed. Informatics.

[142]  Andrew E. Bruno,et al.  The Influence of 3′UTRs on MicroRNA Function Inferred from Human SNP Data , 2011, Comparative and functional genomics.

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

[144]  Sebastian D. Mackowiak,et al.  miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades , 2011, Nucleic acids research.

[145]  Charles E. Vejnar,et al.  miRmap: Comprehensive prediction of microRNA target repression strength , 2012, Nucleic acids research.

[146]  A. Ballabio,et al.  Identification of microRNA-regulated gene networks by expression analysis of target genes , 2012, Genome research.

[147]  T. Thum.  MicroRNA therapeutics in cardiovascular medicine , 2012, EMBO molecular medicine.

[148]  Martin Reczko,et al.  DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways , 2012, Nucleic Acids Res..

[149]  Q. Cui,et al.  Prediction of Disease-Related Interactions between MicroRNAs and Environmental Factors Based on a Semi-Supervised Classifier , 2012, PloS one.

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

[151]  A. Laganà,et al.  miRandola: Extracellular Circulating MicroRNAs Database , 2012, PloS one.

[152]  Jesse D. Ziebarth,et al.  Integrative Analysis of Somatic Mutations Altering MicroRNA Targeting in Cancer Genomes , 2012, PloS one.

[153]  Dai Zhang,et al.  MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs , 2012, BMC Genomics.

[154]  Ivo Grosse,et al.  Functional microRNA targets in protein coding sequences , 2012, Bioinform..

[155]  Isidore Rigoutsos,et al.  Interactive exploration of RNA22 microRNA target predictions , 2012, Bioinform..

[156]  C. K. Hsiao,et al.  miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets , 2012, PloS one.

[157]  Sanghyuk Lee,et al.  miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting , 2012, Nucleic Acids Res..

[158]  C. Norbury,et al.  The Long and Short of MicroRNA , 2013, Cell.

[159]  M. A. Shoorehdeli,et al.  HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens. , 2013, Genomics.

[160]  Martin Reczko,et al.  DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows , 2013, Nucleic Acids Res..

[161]  C. Croce,et al.  Clinical Applications for microRNAs in Cancer , 2013, Clinical pharmacology and therapeutics.

[162]  R. Shankar,et al.  miReader: Discovering Novel miRNAs in Species without Sequenced Genome , 2013, PloS one.

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

[164]  C. Franceschi,et al.  MicroRNAs linking inflamm-aging, cellular senescence and cancer , 2013, Ageing Research Reviews.

[165]  Di Wu,et al.  miRCancer: a microRNA-cancer association database constructed by text mining on literature , 2013, Bioinform..

[166]  R. Regazzi,et al.  Circulating microRNAs as novel biomarkers for diabetes mellitus , 2013, Nature Reviews Endocrinology.

[167]  Xia Li,et al.  mirTarPri: Improved Prioritization of MicroRNA Targets through Incorporation of Functional Genomics Data , 2013, PloS one.

[168]  William A. Rennie,et al.  CLIP-based prediction of mammalian microRNA binding sites , 2013, Nucleic acids research.

[169]  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..

[170]  Burton B. Yang,et al.  Friend or foe: the role of microRNA in chemotherapy resistance , 2013, Acta Pharmacologica Sinica.

[171]  Hong Zheng,et al.  Advances in circulating microRNAs as diagnostic and prognostic markers for ovarian cancer , 2013, Cancer biology & medicine.

[172]  Panayiotis V. Benos,et al.  ComiR: combinatorial microRNA target prediction tool , 2013, Nucleic Acids Res..

[173]  Matthias Blum,et al.  miRmap web: comprehensive microRNA target prediction online , 2013, Nucleic Acids Res..

[174]  C. Sander,et al.  Analysis of microRNA-target interactions across diverse cancer types , 2013, Nature Structural &Molecular Biology.

[175]  Ting Wang,et al.  OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs , 2014, Bioinform..

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

[177]  Chao Wu,et al.  ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context , 2014, Nucleic Acids Res..

[178]  M. Capogrossi,et al.  Admission levels of circulating miR-499-5p and risk of death in elderly patients after acute non-ST elevation myocardial infarction. , 2014, International journal of cardiology.

[179]  Hui Zhou,et al.  starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..

[180]  A. Izzotti,et al.  The effects of environmental chemical carcinogens on the microRNA machinery. , 2014, International journal of hygiene and environmental health.

[181]  Jun Lu,et al.  STarMir: a web server for prediction of microRNA binding sites , 2014, Nucleic Acids Res..

[182]  S. Kauppinen,et al.  Development of microRNA therapeutics is coming of age , 2014, EMBO molecular medicine.

[183]  Ya-Nan Zhao,et al.  Circulating MicroRNAs in gynecological malignancies: from detection to prediction , 2014, Experimental Hematology & Oncology.

[184]  M. Latronico,et al.  microRNAs in cardiovascular diseases: current knowledge and the road ahead. , 2014, Journal of the American College of Cardiology.

[185]  Yang Li,et al.  HMDD v2.0: a database for experimentally supported human microRNA and disease associations , 2013, Nucleic Acids Res..

[186]  H. Taylor,et al.  MicroRNA and gynecological reproductive diseases. , 2014, Fertility and sterility.

[187]  Zhonghan Li,et al.  Therapeutic targeting of microRNAs: current status and future challenges , 2014, Nature Reviews Drug Discovery.

[188]  Hsien-Da Huang,et al.  miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions , 2013, Nucleic Acids Res..

[189]  Michal Linial,et al.  miRror-Suite: decoding coordinated regulation by microRNAs , 2014, Database J. Biol. Databases Curation.

[190]  C. Akdis,et al.  MicroRNAs in Allergy and Asthma , 2014, Current Allergy and Asthma Reports.

[191]  Yan Cui,et al.  PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways , 2013, Nucleic Acids Res..

[192]  P. Vivas-Mejia,et al.  Upregulation of miR-21 in Cisplatin Resistant Ovarian Cancer via JNK-1/c-Jun Pathway , 2014, PloS one.

[193]  D. Bartel,et al.  Predicting effective microRNA target sites in mammalian mRNAs , 2015, eLife.

[194]  Athanasios Fevgas,et al.  DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions , 2014, Nucleic Acids Res..

[195]  Artemis G. Hatzigeorgiou,et al.  DIANA-miRPath v3.0: deciphering microRNA function with experimental support , 2015, Nucleic Acids Res..

[196]  Yan Cui,et al.  miR2GO: comparative functional analysis for microRNAs , 2015, Bioinform..

[197]  Xiaowei Wang,et al.  miRDB: an online resource for microRNA target prediction and functional annotations , 2014, Nucleic Acids Res..