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smiRNAdb specifications

Information


Unique identifier OMICS_27306
Name smiRNAdb
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publication for smiRNAdb

smiRNAdb citations

 (5)
library_books

High throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research

2013
BMC Genomics
PMCID: 3870990
PMID: 24160351
DOI: 10.1186/1471-2164-14-735

[…] ontaining miRNAs. Sequences from 15 different databases were included [], miRBase [], miRNAMap [], microRNA.org [], Argonaute, ASRP [], CSRDB [], fRNAdb [], ncRNAdb [], NONCODE [], RFAM [], RNAdb [], smiRNAdb [], TarBase [], UCSC Genome Browser human miRNAs []. Similarity search was performed using WU-BLAST v.2.2.6 with the DUST filter turned on, wordsize 6, and minimum e-value of 0.0001. Results […]

library_books

Integrative Approaches for microRNA Target Prediction: Combining Sequence Information and the Paired mRNA and miRNA Expression Profiles

2013
PMCID: 3583062
PMID: 23467572
DOI: 10.2174/1574893611308010008

[…] and displays the expression correlations between miRNA-mRNA pairs. The rank list of target mRNAs sorted by their correlations with the corresponding miRNA could also be provided. MirZ [] incorporates smiRNAdb, a database containning miRNA sequencing profiles, and the ElMMo miRNA target prediction algorithm. It also integrates mRNA expression data and allow user to restrict the target prediction to […]

library_books

Integrative transcriptome analysis suggest processing of a subset of long non coding RNAs to small RNAs

2012
Biol Direct
PMCID: 3477000
PMID: 22871084
DOI: 10.1186/1745-6150-7-25

[…] as a ready resource to understand tissue-specific differential expression at each of the small RNA cluster loci. In addition, we also downloaded an independent dataset of small RNA cloning data from smiRNAdb []. The dataset consisted of 60,355 loci derived from 170 tissues. Further, we obtained 4 small RNA datasets from ENCODE project which contained small RNA cluster tags for 2 cell lines (Gm128 […]

call_split

Genetic Association and Altered Gene Expression of Mir 155 in Multiple Sclerosis Patients

2011
Int J Mol Sci
PMCID: 3257096
PMID: 22272099
DOI: 10.3390/ijms12128695
call_split See protocol

[…] re, http://pngu.mgh.harvard.edu/~purcell/plink/The Haploview software, http://www.broad.mit.edu/mpg/haploview/The University of California Santa Cruz Genome Browser (UCSC), http://genome.ucsc.edu/The smiRNAdb repository, http://www.mirz.unibas.ch/cloningprofiles/The miRNA MAP website, http://mirnamap.mbc.nctu.edu.tw/The GeneCards website, http://www.genecards.org/The dbGaP database, http://www.ncb […]

library_books

Databases and resources for human small non coding RNAs

2011
Hum Genomics
PMCID: 3500172
PMID: 21504869
DOI: 10.1186/1479-7364-5-3-192

[…] MirZ [] (Table ), which provides analysis tools for mining various datasets from sequencing projects [] (Table ) and miRNA expression profiles. MirZ integrates two previously developed resources, the smiRNAdb miRNA expression atlas [] and the E1MMo miRNA target prediction algorithm [].Although it is generally assumed that a single precursor miRNA molecule leads to a single functional miRNA, there […]

Citations

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smiRNAdb institution(s)
Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, USA; Biozentrum, University of Basel, Basel, Switzerland; [etc.]
smiRNAdb funding source(s)
Supported by NIH grant P01 GM073047-01 and Howard Hughes Medical Institute, by the SNF grant 205321-105945 and by the Associazione Italiana per la Ricerca sul Cancro (AIRC).

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