smiRNAdb | Tool name | smiRNAdb |
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| URL | http://www.mirz.unibas.ch/cloningprofiles/ |
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| Important features | Online resource for expression information on small RNAs (mostly miRNAs) for human, mouse, rat, zebrafish, worm and fruitfly. |
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| Citations | Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice
A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S,
Fo\E0 R, Schliwka J, Fuchs U, Novosel A, MFCller RU, Schermer B, Bissels U, Inman J,
Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung
V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE,
Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ,
Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. A mammalian
microRNA expression atlas based on small RNA library sequencing. Cell. 2007 Jun
29;129(7):1401-14. PubMed PMID: 17604727; PubMed Central PMCID: PMC2681231.
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| Year of publication | 2007 |
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| Rank by usage frequency | 100 |
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| Comments | Datasets downloadable |
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| Function | FUNCTIONAL ANALYSIS: regulation/ expression, SPECIES: rat, SPECIES: mouse, SPECIES: zebrafish, SPECIES: worm, SPECIES: fly, SPECIES: miscellaneous, http://www.mirz.unibas.ch/cloningprofiles/, Online resource for expression information on small RNAs (mostly miRNAs) for human- mouse- rat- zebrafish- worm and fruitfly. , Landgraf P- Rusu M- Sheridan R- Sewer A- Iovino N- Aravin A- Pfeffer S- Rice
A- Kamphorst AO- Landthaler M- Lin C- Socci ND- Hermida L- Fulci V- Chiaretti S-
Fo\E0 R- Schliwka J- Fuchs U- Novosel A- MFCller RU- Schermer B- Bissels U- Inman J-
Phan Q- Chien M- Weir DB- Choksi R- De Vita G- Frezzetti D- Trompeter HI- Hornung
V- Teng G- Hartmann G- Palkovits M- Di Lauro R- Wernet P- Macino G- Rogler CE-
Nagle JW- Ju J- Papavasiliou FN- Benzing T- Lichter P- Tam W- Brownstein MJ-
Bosio A- Borkhardt A- Russo JJ- Sander C- Zavolan M- Tuschl T. A mammalian
microRNA expression atlas based on small RNA library sequencing. Cell. 2007 Jun
29;129(7):1401-14. PubMed PMID: 17604727; PubMed Central PMCID: PMC2681231.
, 2007, 100, Datasets downloadable, Online, I. SPECIES SUPPORTED INCLUDE: human- mouse- rat- zebrafish- worm and fruitfly II. QUERY OR INPUT DATA: 1. Select microRNAs for visualization of expression profile. 2. Compare two sets of data based on mature miRNAs- mature miRNA sequence groups or precursor clusters or by uploading list of microRNAs 3. .Enter sequence of choice to retrieve homologous sequences. 4. Choose from additional tools such as Sample clustering- Sample PCA- Composition counts etc.
III. OUTPUT DATA: depends on the type of analysis chosen. such as visualization of miRNA expression profile- set of homologous sequences- sample composition (types of RNA found in the sample) etc IV. ADDITIONAL INFORMATION:: mirZ is the integration of the smiRNAdb microRNA expression atlas and the ElMMo microRNA target prediction algorithm. , Identify target sites in alternatively spliced transcripts., 2.3 FIND TARGET: alternatively spliced transcript |
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