miROrtho: computational survey of microRNA genes

Gerlach, D.; Kriventseva, E. V.; Rahman, N.; Vejnar, C. E.; Zdobnov, E. M.

doi:10.1093/nar/gkn707

Title: miROrtho: computational survey of microRNA genes

Journal Article · 14 October 2008 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkn707 · OSTI ID:1625452

Gerlach, D. ^[1]; Kriventseva, E. V. ^[2]; Rahman, N. ^[2]; Vejnar, C. E. ^[3]; Zdobnov, E. M. ^[4]

Univ. of Geneva (Switzerland); Swiss Inst. of Bioformatics, Lausanne (Switzerland); DOE/OSTI
Univ. of Geneva (Switzerland)
Univ. of Geneva (Switzerland); Swiss Inst. of Bioformatics, Lausanne (Switzerland)
Univ. of Geneva (Switzerland); Swiss Inst. of Bioformatics, Lausanne (Switzerland); Imperial College, London (United Kingdom)

MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature ~22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers have been estimated. The miROrtho database (http://cegg.unige. ch/mirortho) presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. We designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data. The miROrtho data are conceptually complementary to the miRBase catalog of experimentally verified miRNA sequences, providing a consistent comparative genomics perspective as well as identifying many novel miRNA genes with strong evolutionary support.

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Research Organization:: USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); University of Geneva (Switzerland)

Sponsoring Organization:: Swiss National Science Foundation (SNF); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI ID:: 1625452

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: Database Vol. 37; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (76)

MicroRNAs and cancer: Profile, profile, profile Barbarotto, Elisa; Schmittgen, Thomas D.; Calin, George A. International Journal of Cancer, Vol. 122, Issue 5 https://doi.org/10.1002/ijc.23343	journal	December 2007
Evidence that miRNAs are different from other RNAs Zhang, B. H.; Pan, X. P.; Cox, S. B. Cellular and Molecular Life Sciences, Vol. 63, Issue 2 https://doi.org/10.1007/s00018-005-5467-7	journal	January 2006
A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes Miranda, Kevin C.; Huynh, Tien; Tay, Yvonne Cell, Vol. 126, Issue 6 https://doi.org/10.1016/j.cell.2006.07.031	journal	September 2006
Identification and characterization of small RNAs involved in RNA silencing Aravin, Alexei; Tuschl, Thomas FEBS Letters, Vol. 579, Issue 26 https://doi.org/10.1016/j.febslet.2005.08.009	journal	August 2005
Genomics of microRNA Kim, V. Narry; Nam, Jin-Wu Trends in Genetics, Vol. 22, Issue 3 https://doi.org/10.1016/j.tig.2006.01.003	journal	March 2006
microRNAs as oncogenes and tumor suppressors Zhang, Baohong; Pan, Xiaoping; Cobb, George P. Developmental Biology, Vol. 302, Issue 1 https://doi.org/10.1016/j.ydbio.2006.08.028	journal	February 2007
Secondary Structure Prediction for Aligned RNA Sequences Hofacker, Ivo L.; Fekete, Martin; Stadler, Peter F. Journal of Molecular Biology, Vol. 319, Issue 5 https://doi.org/10.1016/s0022-2836(02)00308-x	journal	June 2002
Prediction of Mammalian MicroRNA Targets Lewis, Benjamin P.; Shih, I-hung; Jones-Rhoades, Matthew W. Cell, Vol. 115, Issue 7 https://doi.org/10.1016/s0092-8674(03)01018-3	journal	December 2003
The functions of animal microRNAs Ambros, Victor Nature, Vol. 431, Issue 7006 https://doi.org/10.1038/nature02871	journal	September 2004
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals Xie, Xiaohui; Lu, Jun; Kulbokas, E. J. Nature, Vol. 434, Issue 7031 https://doi.org/10.1038/nature03441	journal	February 2005
Identification of hundreds of conserved and nonconserved human microRNAs Bentwich, Isaac; Avniel, Amir; Karov, Yael Nature Genetics, Vol. 37, Issue 7 https://doi.org/10.1038/ng1590	journal	June 2005
MicroRNA signatures in human cancers Calin, George A.; Croce, Carlo M. Nature Reviews Cancer, Vol. 6, Issue 11 https://doi.org/10.1038/nrc1997	journal	November 2006
Prediction of locally stable RNA secondary structures for genome-wide surveys Hofacker, I. L.; Priwitzer, B.; Stadler, P. F. Bioinformatics, Vol. 20, Issue 2 https://doi.org/10.1093/bioinformatics/btg388	journal	January 2004
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
Rfam: annotating non-coding RNAs in complete genomes Griffiths-Jones, S. Nucleic Acids Research, Vol. 33, Issue Database issue https://doi.org/10.1093/nar/gki081	journal	December 2004
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs Nam, J. -W.; Kim, J.; Kim, S. -K. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl321	journal	July 2006
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features Jiang, P.; Wu, H.; Wang, W. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm368	journal	May 2007
OrthoDB: the hierarchical catalog of eukaryotic orthologs Kriventseva, E. V.; Rahman, N.; Espinosa, O. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm845	journal	December 2007
R-Coffee: a method for multiple alignment of non-coding RNA Wilm, A.; Higgins, D. G.; Notredame, C. Nucleic Acids Research, Vol. 36, Issue 9 https://doi.org/10.1093/nar/gkn174	journal	March 2008
The microRNAs of Caenorhabditis elegans Lim, L. P. Genes & Development, Vol. 17, Issue 8 https://doi.org/10.1101/gad.1074403	journal	April 2003
Specificity of microRNA target selection in translational repression Doench, J. G. Genes & Development, Vol. 18, Issue 5 https://doi.org/10.1101/gad.1184404	journal	March 2004
ProbCons: Probabilistic consistency-based multiple sequence alignment Do, C. B. Genome Research, Vol. 15, Issue 2, p. 330-340 https://doi.org/10.1101/gr.2821705	journal	January 2005
Identification of clustered microRNAs using an ab initio prediction method Sewer, Alain; Paul, Nicodème; Landgraf, Pablo BMC Bioinformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2105-6-267	journal	November 2005
microPrimer: the biogenesis and function of microRNA Du, T. Development, Vol. 132, Issue 21 https://doi.org/10.1242/dev.02070	journal	September 2005
Identification of Drosophila MicroRNA Targets Stark, Alexander; Brennecke, Julius; Russell, Robert B. PLoS Biology, Vol. 1, Issue 3 https://doi.org/10.1371/journal.pbio.0000060	journal	October 2003
Principles of MicroRNA–Target Recognition Brennecke, Julius; Stark, Alexander; Russell, Robert B. PLoS Biology, Vol. 3, Issue 3 https://doi.org/10.1371/journal.pbio.0030085	journal	February 2005
miRBase: tools for microRNA genomics. Griffiths-Jones, Sam; Saini, Harpreet Kaur; Van Dongen, Stijn Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.15548	text	January 2008
MicroRNAs as Oncogenes and Tumor Suppressors Rufino-Palomares, Eva E.; Reyes-Zurita, Fernando J.; Lupiáñez, Jose Antonio MicroRNAs in Medicine https://doi.org/10.1002/9781118300312.ch14	book	January 2013
MicroRNAs and cancer: Profile, profile, profile Barbarotto, Elisa; Schmittgen, Thomas D.; Calin, George A. International Journal of Cancer, Vol. 122, Issue 5 https://doi.org/10.1002/ijc.23343	journal	December 2007
Evidence that miRNAs are different from other RNAs Zhang, B. H.; Pan, X. P.; Cox, S. B. Cellular and Molecular Life Sciences, Vol. 63, Issue 2 https://doi.org/10.1007/s00018-005-5467-7	journal	January 2006
Secondary Structure Prediction for Aligned RNA Sequences Hofacker, Ivo L.; Fekete, Martin; Stadler, Peter F. Journal of Molecular Biology, Vol. 319, Issue 5 https://doi.org/10.1016/S0022-2836(02)00308-X	journal	June 2002
Prediction of Mammalian MicroRNA Targets Lewis, Benjamin P.; Shih, I-hung; Jones-Rhoades, Matthew W. Cell, Vol. 115, Issue 7 https://doi.org/10.1016/S0092-8674(03)01018-3	journal	December 2003
MicroRNAs Bartel, David P. Cell, Vol. 116, Issue 2 https://doi.org/10.1016/S0092-8674(04)00045-5	journal	January 2004
Computational and Experimental Identification of C. elegans microRNAs Grad, Yonatan; Aach, John; Hayes, Gabriel D. Molecular Cell, Vol. 11, Issue 5 https://doi.org/10.1016/S1097-2765(03)00153-9	journal	May 2003
Phylogenetic Shadowing and Computational Identification of Human microRNA Genes Berezikov, Eugene; Guryev, Victor; van de Belt, José Cell, Vol. 120, Issue 1 https://doi.org/10.1016/j.cell.2004.12.031	journal	January 2005
A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes Miranda, Kevin C.; Huynh, Tien; Tay, Yvonne Cell, Vol. 126, Issue 6 https://doi.org/10.1016/j.cell.2006.07.031	journal	September 2006
Identification and characterization of small RNAs involved in RNA silencing Aravin, Alexei; Tuschl, Thomas FEBS Letters, Vol. 579, Issue 26 https://doi.org/10.1016/j.febslet.2005.08.009	journal	August 2005
Genomics of microRNA Kim, V. Narry; Nam, Jin-Wu Trends in Genetics, Vol. 22, Issue 3 https://doi.org/10.1016/j.tig.2006.01.003	journal	March 2006
microRNAs as oncogenes and tumor suppressors Zhang, Baohong; Pan, Xiaoping; Cobb, George P. Developmental Biology, Vol. 302, Issue 1 https://doi.org/10.1016/j.ydbio.2006.08.028	journal	February 2007
Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals Xie, Xiaohui; Lu, Jun; Kulbokas, E. J. Nature, Vol. 434, Issue 7031 https://doi.org/10.1038/nature03441	journal	February 2005
Identification of hundreds of conserved and nonconserved human microRNAs Bentwich, Isaac; Avniel, Amir; Karov, Yael Nature Genetics, Vol. 37, Issue 7 https://doi.org/10.1038/ng1590	journal	June 2005
MicroRNA signatures in human cancers Calin, George A.; Croce, Carlo M. Nature Reviews Cancer, Vol. 6, Issue 11 https://doi.org/10.1038/nrc1997	journal	November 2006
A sand fly salivary protein acts as a neutrophil chemoattractant Guimaraes-Costa, Anderson B.; Shannon, John P.; Waclawiak, Ingrid Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-23002-5	journal	May 2021
Lipid and DHA-production in Aurantiochytrium sp. – Responses to nitrogen starvation and oxygen limitation revealed by analyses of production kinetics and global transcriptomes Heggeset, Tonje M. B.; Ertesvåg, Helga; Liu, Bin Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-55902-4	journal	December 2019
A novel lncRNA as a positive regulator of carotenoid biosynthesis in Fusarium Parra-Rivero, Obdulia; Pardo-Medina, Javier; Gutiérrez, Gabriel Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-57529-2	journal	January 2020
From The Cover: Fast and reliable prediction of noncoding RNAs Washietl, S.; Hofacker, I. L.; Stadler, P. F. Proceedings of the National Academy of Sciences, Vol. 102, Issue 7 https://doi.org/10.1073/pnas.0409169102	journal	January 2005
Recent developments in the MAFFT multiple sequence alignment program Katoh, K.; Toh, H. Briefings in Bioinformatics, Vol. 9, Issue 4 https://doi.org/10.1093/bib/bbn013	journal	March 2008
Prediction of locally stable RNA secondary structures for genome-wide surveys Hofacker, I. L.; Priwitzer, B.; Stadler, P. F. Bioinformatics, Vol. 20, Issue 2 https://doi.org/10.1093/bioinformatics/btg388	journal	January 2004
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences Bonnet, E.; Wuyts, J.; Rouze, P. Bioinformatics, Vol. 20, Issue 17 https://doi.org/10.1093/bioinformatics/bth374	journal	June 2004
RNAshapes: an integrated RNA analysis package based on abstract shapes Steffen, P.; Voss, B.; Rehmsmeier, M. Bioinformatics, Vol. 22, Issue 4 https://doi.org/10.1093/bioinformatics/btk010	journal	December 2005
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
Reliable prediction of Drosha processing sites improves microRNA gene prediction Helvik, S. A.; Snove, O.; Saetrom, P. Bioinformatics, Vol. 23, Issue 2 https://doi.org/10.1093/bioinformatics/btl570	journal	November 2006
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures Ng, Kwang Loong Stanley; Mishra, Santosh K. Bioinformatics, Vol. 23, Issue 11 https://doi.org/10.1093/bioinformatics/btm026	journal	January 2007
Rfam: annotating non-coding RNAs in complete genomes Griffiths-Jones, S. Nucleic Acids Research, Vol. 33, Issue Database issue https://doi.org/10.1093/nar/gki081	journal	December 2004
PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology Saebo, P. E.; Andersen, S. M.; Myrseth, J. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki423	journal	July 2005
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs Nam, J. -W.; Kim, J.; Kim, S. -K. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl321	journal	July 2006
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features Jiang, P.; Wu, H.; Wang, W. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm368	journal	May 2007
OrthoDB: the hierarchical catalog of eukaryotic orthologs Kriventseva, E. V.; Rahman, N.; Espinosa, O. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm845	journal	December 2007
miRBase: tools for microRNA genomics Griffiths-Jones, S.; Saini, H. K.; van Dongen, S. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm952	journal	December 2007
R-Coffee: a method for multiple alignment of non-coding RNA Wilm, A.; Higgins, D. G.; Notredame, C. Nucleic Acids Research, Vol. 36, Issue 9 https://doi.org/10.1093/nar/gkn174	journal	March 2008
The microRNAs of Caenorhabditis elegans Lim, L. P. Genes & Development, Vol. 17, Issue 8 https://doi.org/10.1101/gad.1074403	journal	April 2003
Specificity of microRNA target selection in translational repression Doench, J. G. Genes & Development, Vol. 18, Issue 5 https://doi.org/10.1101/gad.1184404	journal	March 2004
ProbCons: Probabilistic consistency-based multiple sequence alignment Do, C. B. Genome Research, Vol. 15, Issue 2, p. 330-340 https://doi.org/10.1101/gr.2821705	journal	January 2005
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis Berezikov, E.; van Tetering, G.; Verheul, M. Genome Research, Vol. 16, Issue 10 https://doi.org/10.1101/gr.5159906	journal	October 2006
Vertebrate MicroRNA Genes Lim, L. P. Science, Vol. 299, Issue 5612 https://doi.org/10.1126/science.1080372	journal	March 2003
Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome Boffelli, D. Science, Vol. 299, Issue 5611 https://doi.org/10.1126/science.1081331	journal	February 2003
MUSCLE: a multiple sequence alignment method with reduced time and space complexity Edgar, Robert C. BMC Bioinformatics, Vol. 5, Issue 1, p. 113 https://doi.org/10.1186/1471-2105-5-113	journal	August 2004
Identification of clustered microRNAs using an ab initio prediction method Sewer, Alain; Paul, Nicodème; Landgraf, Pablo BMC Bioinformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2105-6-267	journal	November 2005
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine Xue, Chenghai; Li, Fei; He, Tao BMC Bioinformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2105-6-310	journal	December 2005
Computational identification of DrosophilamicroRNA genes Lai, Eric C.; Tomancak, Pavel; Williams, Robert W. Genome Biology, Vol. 4, Issue 7, p. R42 https://doi.org/10.1186/gb-2003-4-7-r42	journal	January 2003
Computational and transcriptional evidence for microRNAs in the honey bee genome Weaver, Daniel B.; Anzola, Juan M.; Evans, Jay D. Genome Biology, Vol. 8, Issue 6 https://doi.org/10.1186/gb-2007-8-6-r97	journal	January 2007
The microRNAs of Caenorhabditis elegans Gaur, Rajesh K.; Rossi, John J. Regulation of Gene Expression by Small RNAs https://doi.org/10.1201/9781420008708-11	book	April 2009
microPrimer: the biogenesis and function of microRNA Du, T. Development, Vol. 132, Issue 21 https://doi.org/10.1242/dev.02070	journal	September 2005
Identification of Drosophila MicroRNA Targets Stark, Alexander; Brennecke, Julius; Russell, Robert B. PLoS Biology, Vol. 1, Issue 3 https://doi.org/10.1371/journal.pbio.0000060	journal	October 2003
Principles of MicroRNA–Target Recognition Brennecke, Julius; Stark, Alexander; Russell, Robert B. PLoS Biology, Vol. 3, Issue 3 https://doi.org/10.1371/journal.pbio.0030085	journal	February 2005
miRBase: tools for microRNA genomics. Griffiths-Jones, Sam; Saini, Harpreet Kaur; Van Dongen, Stijn Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.15548	text	January 2008

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MiRNAs: Biology, Biogenesis, their Web-based Tools, and Databases Tafrihi, Majid; Hasheminasab, Elham MicroRNA, Vol. 8, Issue 1 https://doi.org/10.2174/2211536607666180827111633	journal	November 2018
The Regulatory Roles of Non-coding RNAs in Angiogenesis and Neovascularization From an Epigenetic Perspective Hernández-Romero, Itzel Alejandra; Guerra-Calderas, Lissania; Salgado-Albarrán, Marisol Frontiers in Oncology, Vol. 9 https://doi.org/10.3389/fonc.2019.01091	journal	October 2019

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