| 计算生物学与生物信息学专辑 |
|
|
|
|
| miRDOA:集数据存储与在线分析于一体的综合型microRNA数据库 |
| 李俊娥, 贾利鹃, 闫鹏程, 闫学青, 谢国云, 陈禹保 |
| 北京市计算中心 北京 100094 |
|
| miRDOA:A Integrated Database of MicroRNA Include Data Storage and Online Analysis |
| LI Jun-e, JIA Li-juan, YAN Peng-cheng, YAN Xue-qing, XIE Guo-yun, CHEN Yu-bao |
| Beijing Computing Center, Beijing 100094, China |
引用本文:
李俊娥, 贾利鹃, 闫鹏程, 闫学青, 谢国云, 陈禹保. miRDOA:集数据存储与在线分析于一体的综合型microRNA数据库[J]. 中国生物工程杂志, 2014, 34(11): 1-8.
LI Jun-e, JIA Li-juan, YAN Peng-cheng, YAN Xue-qing, XIE Guo-yun, CHEN Yu-bao. miRDOA:A Integrated Database of MicroRNA Include Data Storage and Online Analysis. China Biotechnology, 2014, 34(11): 1-8.
链接本文:
https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20141101
或
https://manu60.magtech.com.cn/biotech/CN/Y2014/V34/I11/1
|
|
[1] Sun K, Lai E C. Adult-specific functions of animal microRNAs. Nat Rev Genet, 2013,14(8): 535-548.
[2] Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004,116(2): 281-297.
[3] Krek A, Grun D, Poy M N, et al. Combinatorial microRNA target predictions. Nat Genet, 2005,37(5): 495-500.
[4] Lai E C, Posakony J W. The Bearded box, a novel 3' UTR sequence motif, mediates negative post-transcriptional regulation of bearded and enhancer of split complex gene expression. Development, 1997,124(23): 4847-4856.
[5] Flynt A S, Lai E C. Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet, 2008,9(11): 831-842.
[6] Hsu S D, Tseng Y T, Shrestha S, et al. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Research, 2014,42(D1): D78-D85.
[7] Wang X. miRDB: A microRNA target prediction and functional annotation database with a wiki interface. RNA, 2008,14(6):1012-1017.
[8] Garcia D M, Baek D, Shin C, et al. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol, 2011, 18(10):1139-1146.
[9] Bartel D P. MicroRNAs: target recognition and regulatory functions. Cell, 2009, 136(2): 215-233.
[10] Sand M, Skrygan M, Georgas D, et al. The miRNA machinery in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases and benign melanocytic nevi. Cell and Tissue Research, 2012, 350(1): 119-126.
[11] Wienholds E, Plasterk R H. MicroRNA function in animal development. FEBS Letters, 2005, 579(26): 5911-5922.
[12] Friedman R C, Farh K K, Burge C B, et al. Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 2009, 19(1): 92-105.
[13] Farazi T A, Spitzer J L, Morozov P, et al. miRNAs in human cancer. The Journal of Pathology, 2011, 223(2): 102-115.
[14] Huang J, Wang J, Srivastava V, et al. MicroRNA machinery genes as novel biomarkers for cancer. Frontiers in Oncology, 2014,19(4):113.
[15] Wang J, Czech B, Crunk A, et al. Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome research, 2011, 21(9):1462-1477.
[16] Baker M. MicroRNA profiling: separating signal from noise. Nat Meth, 2010, 7(9):687-692.
[17] Desvignes T, Beam M J, Batzel P, et al. Expanding the annotation of zebrafish microRNAs based on small RNA sequencing. Gene, 2014,546(2):386-389.
[18] Tanaka T, Kobayashi F, Joshi G, et al. Next-generation survey sequencing and the molecular organization of wheat chromosome 6B. DNA Res, 2014,21(2):103-114.
[19] Metpally R P, Nasser S, Malenica L, et al. Comparison of analysis tools for mirna high throughput sequencing using nerve crush as a model. Front Genet, 2013, 4:20.
[20] Sandhu S, Garzon R. Potential Applications of MicroRNAs in Cancer Diagnosis, Prognosis, and Treatment. Seminars in Oncology, 2011, 38(6):781-787.
[21] Witten D, Tibshirani R, Gu S, et al. Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls. BMC Biology, 2010, 8(1):58.
[22] Pang M, Woodward A W, Agarwal V, et al. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol, 2009, 10(11):R122.
[23] Zhu Q, Spriggs A, Matthew L, et al. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res, 2008, 18(9):1456 - 1465.
[24] Git A, Dvinge H, Salmon-Divon M, et al. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA, 2010, 16(5): 991-1006.
[25] Griffiths-Jones S, Moxon S, Marshall M, et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research, 2005, 33:D121-D124.
[26] Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research, 2014, 42(D1): D68-D73.
[27] Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res, 2011, 39:D152 - D157.
[28] Zhang Z, Yu J, Li D, et al. PMRD: plant microRNA database. Nucleic Acids Research, 2010, 38(1): D806-D813.
[29] Sun X, Dong B, Yin L, et al. PMTED: a plant microRNA target expression database. BMC Bioinformatics, 2013, 14(1): 174.
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
