YM500v2: A small RNA sequencing (smRNA-seq) database for human cancer miRNome research

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D862-D867

  Cheng, Wei Chung ^a   Chung, I Fang ^b   Tsai, Cheng Fong ^b   Huang, Tse Shun ^c   Chen, Chen Yang ^b   Wang, Shao Chuan ^b   Chang, Ting Yu ^b   Sun, Hsing Jen ^b   Chao, Jeffrey Yung Chuan ^b,d   Cheng, Cheng Chung ^e   Wu, Cheng Wen ^b,f   Wang, Hsei Wei ^b,g  

^a CHINA MEDICAL UNIVERSITY   (Taiwan)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d TAICHUNG VETERANS GENERAL HOSPITAL   (Taiwan)

^e TRI SERVICE GENERAL HOSPITAL   (Taiwan)

^f INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^g TAIPEI CITY HOSPITAL   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; CANCER RESEARCH; COMPUTER PREDICTION; COMPUTER PROGRAM; DATA COLLECTION METHOD; GENETIC ALGORITHM; GENETIC DATABASE; IMMUNOPRECIPITATION; INFORMATION STORAGE; RNA SEQUENCE; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; INTERNET; METABOLISM; NEOPLASM; NUCLEIC ACID DATABASE; SEQUENCE ANALYSIS;

DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; HUMANS; INTERNET; MICRORNAS; NEOPLASMS; SEQUENCE ANALYSIS, RNA;

EID: 84938995518     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1156     Document Type: Article

References (36)

1. Mendell,J. T. and Olson,E. N. (2012) MicroRNAs in stress signaling and human disease. Cell, 148, 1172-1187.
2. Friedman,R. C., Farh,K. K., Burge,C. B. and Bartel,D. P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
3. Adams,B. D., Kasinski,A. L. and Slack,F. J. (2014) Aberrant regulation and function of microRNAs in cancer. Curr. Biol., 24, R762-R776.
4. Lu,J., Getz,G., Miska,E. A., Alvarez-Saavedra,E., Lamb,J., Peck,D., Sweet-Cordero,A., Ebert,B. L., Mak,R. H., Ferrando,A. A. et al. (2005) MicroRNA expression profiles classify human cancers. Nature, 435, 834-838.
5. Liu,C., Kelnar,K., Vlassov,A. V., Brown,D.,Wang,J. and Tang,D. G. (2012) Distinct microRNA expression profiles in prostate cancer stem/progenitor cells and tumor-suppressive functions of let-7. Cancer Res., 72, 3393-3404.
6. Andorfer,C. A., Necela,B. M., Thompson,E. A. and Perez,E. A. (2011) MicroRNA signatures: clinical biomarkers for the diagnosis and treatment of breast cancer. Trends Mol. Med., 17, 313-319.
7. Farazi,T. A., Ten Hoeve,J. J., Brown,M., Mihailovic,A., Horlings,H. M., van de Vijver,M. J., Tuschl,T. and Wessels,L. F. (2014) Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets. Genome Biol., 15, R9.
8. Garzon,R., Volinia,S., Liu,C. G., Fernandez-Cymering,C., Palumbo,T., Pichiorri,F., Fabbri,M., Coombes,K., Alder,H., Nakamura,T. et al. (2008) MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. Blood, 111, 3183-3189.
9. Hayes,J., Peruzzi,P. P. and Lawler,S. (2014) MicroRNAs in cancer: biomarkers, functions and therapy. Trends Mol. Med., 20, 460-469.
10. Yin,H., Kanasty,R. L., Eltoukhy,A. A., Vegas,A. J., Dorkin,J. R. and Anderson,D. G. (2014) Non-viral vectors for gene-based therapy. Nat. Rev. Genet., 15, 541-555.
11. van Rooij,E. and Kauppinen,S. (2014) Development of microRNA therapeutics is coming of age. EMBO Mol. Med., 6, 851-864.
12. Li,Z. and Rana,T. M. (2014) Therapeutic targeting of microRNAs: current status and future challenges. Nat. Rev. Drug Discov., 13, 622-638.
13. Bader,A. G., Brown,D. and Winkler,M. (2010) The promise of microRNA replacement therapy. Cancer Res., 70, 7027-7030.
14. Bouchie,A. (2013) First microRNA mimic enters clinic. Nat. Biotechnol., 31, 577-577.
15. Cheng,W. C., Chung,I. F., Huang,T. S., Chang,S. T., Sun,H. J., Tsai,C. F., Liang,M. L., Wong,T. T. and Wang,H. W. (2013) YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res., 41, D285-D294.
16. Friedlander,M. R., Lizano,E., Houben,A. J., Bezdan,D., Banez-Coronel,M., Kudla,G., Mateu-Huertas,E., Kagerbauer,B., Gonzalez,J., Chen,K. C. et al. (2014) Evidence for the biogenesis of more than 1,000 novel human microRNAs. Genome Biol., 15, R57.
17. Ladewig,E., Okamura,K., Flynt,A. S., Westholm,J. O. and Lai,E. C. (2012) Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Res., 22, 1634-1645.
18. Friedlander,M. R., Mackowiak,S. D., Li,N., Chen,W. and Rajewsky,N. (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40, 37-52.
19. Friedlander,M. R., Chen,W., Adamidi,C., Maaskola,J., Einspanier,R., Knespel,S. and Rajewsky,N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
20. Chen,X., Li,Q., Wang,J., Guo,X., Jiang,X., Ren,Z., Weng,C., Sun,G., Wang,X., Liu,Y. et al. (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol., 10, R78.
21. Hackenberg,M., Sturm,M., Langenberger,D., Falcon-Perez,J. M. and Aransay,A. M. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 37, W68-W76.
22. Anders,S. and Huber,W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
23. Anders,S., McCarthy,D. J., Chen,Y., Okoniewski,M., Smyth,G. K., Huber,W. and Robinson,M. D. (2013) Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc., 8, 1765-1786.
24. Boele,J., Persson,H., Shin,J. W., Ishizu,Y., Newie,I. S., Sokilde,R., Hawkins,S. M., Coarfa,C., Ikeda,K., Takayama,K. et al. (2014) PAPD5-mediated 3- adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proc. Natl Acad. Sci. U. S. A., 111, 11467-11472.
25. Fukunaga,R., Han,B. W., Hung,J. H., Xu,J., Weng,Z. and Zamore,P. D. (2012) Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell, 151, 533-546.
26. Wu,H., Ye,C., Ramirez,D. and Manjunath,N. (2009) Alternative processing of primary microRNA transcripts by Drosha generates 5- end variation of mature microRNA. PLoS One, 4, e7566.
27. Ma,H., Wu,Y., Choi,J. G. and Wu,H. (2013) Lower and upper stem-single-stranded RNA junctions together determine the Drosha cleavage site. Proc. Natl Acad. Sci. U. S. A., 110, 20687-20692.
28. Hinton,A., Hunter,S. E., Afrikanova,I., Jones,G. A., Lopez,A. D., Fogel,G. B., Hayek,A. and King,C. C. (2014) sRNA-seq analysis of human embryonic stem cells and definitive endoderm reveal differentially expressed microRNAs and novel isomiRs with distinct targets. Stem Cells, 32, 2360-2372.
29. Tan,G. C., Chan,E., Molnar,A., Sarkar,R., Alexieva,D., Isa,I. M., Robinson,S., Zhang,S., Ellis,P., Langford,C. F. et al. (2014) 5- isomiR variation is of functional and evolutionary importance. Nucleic Acids Res., 42, 9424-9435.
30. Xia,J. and Zhang,W. (2014) A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5-isoforms in four model species. Nucleic Acids Res., 42, 1427-1441.
31. Guo,L., Zhao,Y., Yang,S., Zhang,H. and Chen,F. (2014) A genome-wide screen for non-template nucleotides and isomiR repertoires in miRNAs indicates dynamic and versatile microRNAome. Mol. Biol. Rep., 41, 6649-6658.
32. Guo,L. and Chen,F. (2014) A challenge for miRNA: multiple isomiRs in miRNAomics. Gene, 544, 1-7.
33. Humphreys,D. T. and Suter,C. M. (2013) miRspring: a compact standalone research tool for analyzing miRNA-seq data. Nucleic Acids Res., 41, e147.
34. Giurato,G., De Filippo,M. R., Rinaldi,A., Hashim,A., Nassa,G., Ravo,M., Rizzo,F., Tarallo,R. and Weisz,A. (2013) iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq. BMC Bioinformatics, 14, 362.
35. de Oliveira,L. F., Christoff,A. P. and Margis,R. (2013) isomiRID: a framework to identify microRNA isoforms. Bioinformatics, 29, 2521-2523.
36. Luo,G. Z., Yang,W., Ma,Y. K. and Wang,X. J. (2014) ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. Bioinformatics, 30, 434-436.