微RNA與微RNA靶數據庫

小分子核糖核酸（microRNA，miRNA，微RNA）是一類由內源基因編碼的長度約為22個核苷酸的非編碼單鏈RNA 分子,它們在動植物中參與轉錄後基因表達調控^[1].。microRNA (微RNA)參與各種各樣的生物學過程，包括凋亡、增殖、分化和細胞周期。此外，microRNA(微RNA)還與腫瘤和其他疾病的發生和發展相關。這裏收集了目前比較流行的microRNA（微RNA）基因及其靶基因數據庫，以便大家使用和查詢.

microRNA靶基因數據庫

數據庫名字	數據庫描述	數據庫類型	網頁連結	參考文獻
targetScan	targetScan 搜尋動物的microRNA靶基因。	database,webserver	website （頁面存檔備份，存於互聯網檔案館）	^[2]
starBase	starBase 從高通量的CLIP-Seq實驗數據（CLIP-Seq和HITS-CLIP）和降解組實驗數據中（degradome sequencing）搜尋micorRNA的靶標。提供了各式各樣的可視化界面去探討microRNA的靶標	database	website	^[3]
PicTar	PicTar 聯合的microRNA靶標預測。	database,webserver,predictions	website	^[4]
PITA	PITA基於靶位點的可接性（target-site accessibility）預測microRNA的靶標。	webserver,predictions	predictions （頁面存檔備份，存於互聯網檔案館）	^[5]
RNA22	RNA22基因序列特徵預測microRNA的結合位點。	webserver,predictions	webserver	^[6]
miRecords	一個整合的microRNA靶標數據庫。	database	website	^[7]
TarBase	一個全面收集已被實驗驗證的microRNA靶標數據庫。	database	website	^[8]
miRTarBase	一個全面收集已被實驗驗證的microRNA靶標數據庫。	database	website	^[9]

MicroRNA數據庫

數據庫名字	數據庫描述	數據庫類型	網頁連結	參考文獻
deepBase	deepBase 從新一代測序技術（深度測序技術，deep-sequencing）數據中註釋和鑑定microRNA，piRNA，siRNA基因及長非編碼RNA基因及其他們的表達模式。	database	website	^[10]
miRBase	miRBase 數據庫是查詢和發佈發表的microRNA基因。	database	website （頁面存檔備份，存於互聯網檔案館）	^[11]
microRNA.org	microRNA.org 構建和查詢microRNA的表達模式及microRNA的靶標。	database	website	^[12]
miRGen	miRGen研究動物的microRNA基因組織和功能。	database	website （頁面存檔備份，存於互聯網檔案館）	^[13]
miRNAMap	miRNAMap: 動物microRNA基因的基因組的map和microRNA的靶基因。	database	website	^[14]
PMRD	植物microRNA數據庫	database	website （頁面存檔備份，存於互聯網檔案館）	^[15]
.

參考資料

^ Bartel, DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009, 136 (2): 215–33. PMID 19167326. doi:10.1016/j.cell.2009.01.002.
^ Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.. Cell. 2005, 120 (1): 15–20. PMID 15652477. doi:10.1016/j.cell.2004.12.035.
^ Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.. Nucl. Acids Res. 2010, (Database issue): 1–8. PMID 21037263. doi:10.1093/nar/gkq1056.
^ Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions.. Nat Genet. 2005, 37 (5): 495–500. PMID 15806104. doi:10.1038/ng1536.
^ Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition.. Nat Genet. 2007, 39 (10): 1278–84. PMID 17893677. doi:10.1038/ng2135.
^ Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.. Cell. 2006, 126 (6): 1203–17. PMID 16990141. doi:10.1016/j.cell.2006.07.031.
^ Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions.. Nucl. Acids Res. 2009, 37 (Database issue): D105–110. PMID 18996891. doi:10.1093/nar/gkn851.
^ Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets.. RNA. 2006, 12 (2): 192–197. PMID 16373484. doi:10.1261/rna.2239606.
^ Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD. miRTarBase: a database curates experimentally validated microRNA-target interactions.. Nucleic acids research. 2010, 39 (Database issue): D163–169. PMID 21071411. doi:10.1093/nar/gkq1107.
^ Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply annotating and mining deep sequencing data.. Nucl. Acids Res. 2010, 38 (Database issue): D123–130. PMC 2808990  . PMID 19966272. doi:10.1093/nar/gkp943.
^ Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics.. Nucl. Acids Res. 2008, 36: D154–D158. PMC 2238936  . PMID 17991681. doi:10.1093/nar/gkm952.
^ Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression.. Nucl. Acids Res. 2007, 36 (Database issue): D149–153. PMC 2238905  . PMID 18158296. doi:10.1093/nar/gkm995.
^ Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. miRGen: a database for the study of animal microRNA genomic organization and function.. Nucl. Acids Res. 2007, 35 (Database issue): D149–55. PMC 1669779  . PMID 17108354. doi:10.1093/nar/gkl904.
^ Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.. Nucl. Acids Res. 2006, 34 (Database issue): D135–139. PMC 1347497  . PMID 16381831. doi:10.1093/nar/gkj135.
^ Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. PMRD: plant microRNA database.. Nucl. Acids Res. 2010, 38 (Database issue): D806–813. PMC 2808885  . PMID 19808935. doi:10.1093/nar/gkp818.

延伸閱讀

Lee, RC; Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science. 2001, 294 (5543): 862–864. PMID 11679672. doi:10.1126/science.1065329.
Ambros, V. microRNAs: tiny regulators with great potential. Cell. 2001, 107 (7): 823–826. PMID 11779458. doi:10.1016/S0092-8674(01)00616-X.

外部連結

[1] Bartel, DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009, 136 (2): 215–33. PMID 19167326. doi:10.1016/j.cell.2009.01.002.

[pmid15652477-2] Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.. Cell. 2005, 120 (1): 15–20. PMID 15652477. doi:10.1016/j.cell.2004.12.035.

[pmid21037263-3] Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data.. Nucl. Acids Res. 2010, (Database issue): 1–8. PMID 21037263. doi:10.1093/nar/gkq1056.

[pmid15806104-4] Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, Rajewsky N. Combinatorial microRNA target predictions.. Nat Genet. 2005, 37 (5): 495–500. PMID 15806104. doi:10.1038/ng1536.

[pmid17893677-5] Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition.. Nat Genet. 2007, 39 (10): 1278–84. PMID 17893677. doi:10.1038/ng2135.

[pmid16990141-6] Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.. Cell. 2006, 126 (6): 1203–17. PMID 16990141. doi:10.1016/j.cell.2006.07.031.

[pmid18996891-7] Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions.. Nucl. Acids Res. 2009, 37 (Database issue): D105–110. PMID 18996891. doi:10.1093/nar/gkn851.

[pmid16373484-8] Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets.. RNA. 2006, 12 (2): 192–197. PMID 16373484. doi:10.1261/rna.2239606.

[pmid21071411-9] Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD. miRTarBase: a database curates experimentally validated microRNA-target interactions.. Nucleic acids research. 2010, 39 (Database issue): D163–169. PMID 21071411. doi:10.1093/nar/gkq1107.

[pmid19966272-10] Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply annotating and mining deep sequencing data.. Nucl. Acids Res. 2010, 38 (Database issue): D123–130. PMC 2808990  . PMID 19966272. doi:10.1093/nar/gkp943.

[pmid17991681-11] Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics.. Nucl. Acids Res. 2008, 36: D154–D158. PMC 2238936  . PMID 17991681. doi:10.1093/nar/gkm952.

[pmid18158296-12] Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: targets and expression.. Nucl. Acids Res. 2007, 36 (Database issue): D149–153. PMC 2238905  . PMID 18158296. doi:10.1093/nar/gkm995.

[pmid17108354-13] Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. miRGen: a database for the study of animal microRNA genomic organization and function.. Nucl. Acids Res. 2007, 35 (Database issue): D149–55. PMC 1669779  . PMID 17108354. doi:10.1093/nar/gkl904.

[pmid16381831-14] Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.. Nucl. Acids Res. 2006, 34 (Database issue): D135–139. PMC 1347497  . PMID 16381831. doi:10.1093/nar/gkj135.

[pmid19808935-15] Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. PMRD: plant microRNA database.. Nucl. Acids Res. 2010, 38 (Database issue): D806–813. PMC 2808885  . PMID 19808935. doi:10.1093/nar/gkp818.

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