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Protocols

SylArray specifications

Information


Unique identifier OMICS_14647
Name SylArray
Interface Web user interface
Restrictions to use None
Input data A sorted list of genes from an expression experiment.
Programming languages Java, Perl, R
License GNU General Public License version 3.0
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for SylArray

SylArray citations

 (12)
library_books

Anti miR 17 therapy delays tumorigenesis in MYC driven hepatocellular carcinoma (HCC)

2017
Oncotarget
PMCID: 5814155
PMID: 29464015
DOI: 10.18632/oncotarget.22342

[…] (8831/11427) had measurable expression, in at least one of the six samples; and 67.9% (7758/11427) genes saw measurable expression levels in all six samples. Sylamer analysis was performed through a Sylarray web server []. TargetScan 6.2 was used to identify putative conserved targets of miR-17 []. De-repression in a cell line was defined as upregulation >1.3 fold (p-value<0.05). An absolute fold […]

library_books

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

2015
Nature
PMCID: 4376666
PMID: 25799984
DOI: 10.1038/nature14280

[…] To examine off-target effects of the siRNA, the list of mRNAs was ranked by fold change of mRNA level between untransfected (UT) and knockdown (KD) condition and analyzed by SylArray using “Use all available words” option. Top 3 significantly enriched motifs were reported to demonstrate that the primary changes in mRNA stability result from off-target effects of the siRNA […]

library_books

Transcriptional targets of the schizophrenia risk gene MIR137

2014
PMCID: 4080323
PMID: 24984191
DOI: 10.1038/tp.2014.42

[…] large increases in expression of miR-137 did not lead to clear alterations in cell fate after 24 or 48 h.We verified the downregulation of predicted targets of miR-137 in two ways. First, we applied Sylarray to the RNA-seq data to evaluate fold change differences associated with all known miRNA seed sequences. Genes with the miR-137 seed sequence (AGCAATTA) in the 3'-untranslated repeat evidenced […]

library_books

The HER2 Encoded miR 4728 3p Regulates ESR1 through a Non Canonical Internal Seed Interaction

2014
PLoS One
PMCID: 4020767
PMID: 24828673
DOI: 10.1371/journal.pone.0097200

[…] d over-represented stretches of consecutive bases (“words”) in the 3' untranslated regions (UTRs) of genes from ranked gene lists and calculated the statistical significance of their enrichment using SylArray . Unsurprisingly, the strongest signals detected among down regulated genes corresponded to words complementary to the transfected miRNAs. But while down regulation of genes carrying canonica […]

library_books

Quantitative Proteomic Analysis of Gene Regulation by miR 34a and miR 34c

2014
PLoS One
PMCID: 3956911
PMID: 24637697
DOI: 10.1371/journal.pone.0092166

[…] s in the coding sequence or targets without seed matches are not included. Thus, the true number of direct targets is probably higher.A nucleotide motif enrichment analysis employing the online tool “Sylarray” revealed that not only the signal for the mature miRNA but also the *strand seed of the respective miR-34 member was detectable (). Recent studies suggest that the incorporation of the *str […]

call_split

Hmga2 functions as a competing endogenous RNA to promote lung cancer progression

2013
Nature
PMCID: 3886898
PMID: 24305048
DOI: 10.1038/nature12785
call_split See protocol

[…] ts expressed in the samples described above. This set of transcripts was then placed in rank order by their differential expression between two groups and analysed using the Sylamer algorithm via the SylArray platform. A Sylamer plot was then generated for all 8mer miRNA strings whose target sites were enriched significantly (p<0.001 by hypergeometric testing). […]

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SylArray institution(s)
EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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