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Protocols

RNAplex specifications

Information


Unique identifier OMICS_09345
Name RNAplex
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for RNAplex

RNAplex citations

 (55)
library_books

Long non coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

2018
BMC Plant Biol
PMCID: 5936019
PMID: 29728055
DOI: 10.1186/s12870-018-1288-3

[…] as annotated by scanning 2000 bp upstream or downstream of genes based on the switchgrass genomic database [–], and then analyzing complementary base-pairing between antisense lncRNAs and mRNAs using RNAplex software []. In this study, 4554 lncRNAs were annotated, and 9.7% (441) of these were differentially expressed (Table ; Fig. ). We analyzed the functions of the predicted target genes of all l […]

library_books

Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells

2018
PLoS One
PMCID: 5892903
PMID: 29634734
DOI: 10.1371/journal.pone.0195468

[…] omosomes or distal regions)[], and lncRNA-mRNA interaction can affect mRNA level [,]. In this study, 20 DE-lncRNAs with the lowest FDR values were selected for prediction of their trans-target genes. RNAplex [] was used for searching interactions between above mentioned lncRNAs and differentially expressed mRNAs (DE-mRNAs). It showed that 20 DE-lncRNAs have 1098 potential trans-target mRNAs ().The […]

library_books

Regulation of Long Noncoding RNAs Responsive to Phytoplasma Infection in Paulownia tomentosa

2018
Int J Genomics
PMCID: 5841072
PMID: 29675420
DOI: 10.1155/2018/3174352

[…] NA-mRNA duplex energy. First, BLASTN searches were performed to detect potential target mRNA sequences complementary to the lncRNA sequences with identity > 95% and E value < 1E − 5. Then we used the RNAplex software to calculate the complementary energy between the lncRNAs and their potential transregulated target genes with RNAplex − E −30. […]

library_books

Assessment of Bona Fide sRNAs in Staphylococcus aureus

2018
Front Microbiol
PMCID: 5826253
PMID: 29515534
DOI: 10.3389/fmicb.2018.00228

[…] NApredator website (Eggenhofer et al., ) was used to predict sRNA-mRNA interactions between the sRNAs from Table and the NCTC8325 genome (accession # NC_007795). In the absence of conservation data, RNAplex program used by RNA predator is among the best predictor (Pain et al., ). Results are presented in Data Sheet . […]

library_books

Silencing of Long Non coding RNA MIAT Sensitizes Lung Cancer Cells to Gefitinib by Epigenetically Regulating miR 34a

2018
Front Pharmacol
PMCID: 5816758
PMID: 29487526
DOI: 10.3389/fphar.2018.00082

[…] Bioinformatics analysis was used to search for the potential targeted microRNAs of lncRNA MIAT, such as MiRcode, RNAplex, catRAPID omics. Together, miR-34a was found to be a conserved target of lncRNA MIAT. To investigate if the predicted binding site of miR-34a to 3′UTR of lncRNA MIAT is responsible for this re […]

library_books

Competitive endogenous RNA networks: integrated analysis of non coding RNA and mRNA expression profiles in infantile hemangioma

2018
Oncotarget
PMCID: 5844720
PMID: 29552284
DOI: 10.18632/oncotarget.23946

[…] g sense transcripts. Transcripts that overlapped with LncRNAs on the opposite strand were also identified as lncRNA target genes, and the interactions between lncRNAs and transcripts were revealed by RNAplex []. […]

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RNAplex institution(s)
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
RNAplex funding source(s)
This work was supported by siemens, by the Wiener Wissenschafts-, Technologie- und Forschungsfonds and by the Austrian GEN-AU projects bioinformatics integration network and non-coding RNA.

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