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smiRNAdb specifications


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


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

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

[…] ontaining miRNAs. Sequences from 15 different databases were included [], miRBase [], miRNAMap [], [], 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 […]


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

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 […]


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

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 […]


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

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

[…] re, Haploview software, University of California Santa Cruz Genome Browser (UCSC), smiRNAdb repository, miRNA MAP website, GeneCards website, dbGaP database, http://www.ncb […]


Databases and resources for human small non coding RNAs

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 […]


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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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