Links
miRNA interaction databases:| TargetScan | Most Mammalian mRNAs Are Conserved Targets of MicroRNAs, Robin C Friedman, Kyle Kai-How Farh, Christopher B Burge, David P Bartel., Genome Research, 19:92-105 (2009). |
| miRanda | The microRNA.org resource: targets and expression., Betel D, Wilson M, Gabow A, Marks DS, Sander C., Nucleic Acids Res. 2008 Jan; 36(Database Issue): D149-53. |
| PICTAR | microRNA target predictions in vertebrates, Krek et al, Nature Genetics 37:495-500 (2005) |
| PITA | The role of site accessibility in microRNA target recognition, Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul & Eran Segal, Nature Genetics 39, 1278 - 1284 (2007) |
| miRDB | miRDB: a microRNA target prediction and functional annotation database with a wiki interface., Xiaowei Wang, RNA 14(6):1012-1017 |
| TarBase | The database of experimentally supported targets: a functional update of TarBase. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG., Nucleic Acids Res. 2009 Jan;37(Database issue):D155-8. Epub 2008 Oct 27. |
| miRecords | miRecords: an integrated resource for microRNA-target interactions., Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T, Nucleic Acids Res. 2009, 37: D105-D110. |
ncRNA Annotation databases:
| miRBase | miRBase: integrating microRNA annotation and deep-sequencing data., Kozomara A, Griffiths-Jones S., NAR 2011 39(Database Issue):D152-D157 |
| Rfam | Rfam 11.0: 10 years of RNA families., Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A., Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3. |
| UCSC table browser | The UCSC Table Browser data retrieval tool., Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ., Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. |
Genomes:
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Homo sapiens (hg19): UCSC Genome browser |
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006. |
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Mus musculus (mm10): UCSC Genome browser |
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006. |
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Arabidopsis thaliana (TAIR9): The Arabidopsis Information Resource |
The Arabidopsis Information Resource |
Differential Expression:
| DEseq | Differential expression analysis for sequence count data, Simon Anders, Wolfgang Huber, Genome Biology 11 (2010) R106, doi:10.1186/gb-2010-11-10-r106 |
microRNA prediction:
| miRDeep | Discovering microRNAs from deep sequencing data using miRDeep, Friedländer, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., Rajewsky, N., Nature Biotechnology, 26, 407-415 (2008) |