miRTargetLink—miRNAs, Genes and Interaction Networks

Hamberg, Maarten; Backes, Christina; Fehlmann, Tobias; Hart, Martin; Meder, Benjamin; Meese, Eckart; Keller, Andreas

doi:10.3390/ijms17040564

Cited by 104 publications

(108 citation statements)

References 15 publications

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“…With the predictions, we extracted the context++ scores and used them for prioritizing the targets, miRNA-target interactions with context++ scores below 1 were considered as high-likelihood targets. Target networks were constructed using an offline version of MiRTargetLink [22] and visualized in Cytoscape. miRNA target pathway analysis has been carried out using GeneTrai2 [23].…”

Section: Methodsmentioning

confidence: 99%

cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

et al. 2016

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BackgroundWe present the first sequencing data using the combinatorial probe-anchor synthesis (cPAS)-based BGISEQ-500 sequencer. Applying cPAS, we investigated the repertoire of human small non-coding RNAs and compared it to other techniques.ResultsStarting with repeated measurements of different specimens including solid tissues (brain and heart) and blood, we generated a median of 30.1 million reads per sample. 24.1 million mapped to the human genome and 23.3 million to the miRBase. Among six technical replicates of brain samples, we observed a median correlation of 0.98. Comparing BGISEQ-500 to HiSeq, we calculated a correlation of 0.75. The comparability to microarrays was similar for both BGISEQ-500 and HiSeq with the first one showing a correlation of 0.58 and the latter one correlation of 0.6. As for a potential bias in the detected expression distribution in blood cells, 98.6% of HiSeq reads versus 93.1% of BGISEQ-500 reads match to the 10 miRNAs with highest read count. After using miRDeep2 and employing stringent selection criteria for predicting new miRNAs, we detected 74 high-likely candidates in the cPAS sequencing reads prevalent in solid tissues and 36 candidates prevalent in blood.ConclusionsWhile there is apparently no ideal platform for all challenges of miRNome analyses, cPAS shows high technical reproducibility and supplements the hitherto available platforms.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0287-1) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

et al. 2016

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“…Moreover, the miR-92a is involved in the regulation of several genes. MiRTargetLink [78], using information from miRTarBase [79,80], found 1419 genes that are targeted by miR-92a: 30 interactions with strong support, 1301 interactions with weak support, and 88 predicted interactions (Table S1). MiR-92a regulates several processes including cell proliferation and the development of cancer [77,81].…”

Section: Discussionmentioning

confidence: 99%

Exosomal miR-92a Concentration in the Serum of Shift Workers

et al. 2020

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Shift work is associated with alterations in the human biological clock and metabolism. Serum exosomal miR-92a concentration was inversely correlated with brown adipose tissue activity playing a pivotal role in energy balance. In this study, miR-92a was measured in serum exosomes of 30 workers engaged in shift and daytime work. No significant metabolic alterations were shown between daytime and shift workers while a difference in serum exosomal miR-92a levels was found between the two groups. The lower levels of miR-92a in shift workers were suggestive of a higher brown adipose tissue activity compared with daytime workers. However, the possibility that other physiological and pathological processes may influence miR-92a cannot be ruled out. Our results suggest further investigations on brown adipose tissue activity and on miR-92a regulatory mechanisms, such as those related to the estrogen pathway, in shift workers.

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“…For the selected candidate genes, an attempt to retrieve the most miRNA targets was made by searching three reliable and highly cited databases for in-silico studies and miRNA target search namely, MiRWalk (http://mirwalk.umm.uni-heidelberg.de/) (14), MiRNet (https://www.mirnet.ca/miRNet/home.xhtml) (15) and miRTargetLink Human (https://ccbweb.cs.uni-saarland.de/mirtargetlink/) (16). A thorough in-depth search of all the three databases was done without setting up any filters to retrieve all the possible targets.…”

Section: Data Sources and Retrievalmentioning

confidence: 99%

Identification of regulatory microRNAs for hypoxia induced coagulation mechanism byIn-silicoanalysis

Srivastava

2020

Preprint

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BackgroundHypoxia (oxygen deprivation) is known to induce a prothrombotic state by activating the process of coagulation. Hypoxia inducible factor (HIF), is a major transcription factor involved in cellular response to low oxygen tension. MicroRNAs (miRNAs) are non-coding regulatory sequences capable of post-translational modification of multiple genes. Present study aimed to identify common regulatory miRNAs of HIF gene family and coagulation pathway by In-silico approach in order to understand the molecular mechanism underlying the process of hypoxia induced coagulation.MethodsHIF family and Coagulation pathway genes along with their receptors and mediators were enlisted after comprehensive literature review. Thorough search of three highly cited database was done to identify the miRNAs targeting these genes. The extracted miRNA list was then prioritized on the basis of number and functional relevance of genes targeted. The target genes of all prioritized miRNAs were listed and subjected to followed by gene ontology (GO) study and pathway analysis.ResultPresent In-silico analysis identified five candidate miRNAs, viz., hsa-mir-4433a-3p, hsa-mir-4667-5p, hsa-mir-6735-5p, hsa-mir-6777-3p and hsa-mir-6815-3p that co-regulate genes of HIF family and coagulation pathway. GO and pathway analysis revealed that genes regulated by these five microRNAs, predominantly modulate genes facilitating coagulation and hypoxic response.ConclusionWe identified five key microRNAs involved in body’s response to hypoxia and potentially involved in the blood coagulation cascade as well. These five candidate miRNAs may serve as putative epigenetic biomarkers and therapeutic targets to modulate the process of hypoxia induced coagulation.

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miRTargetLink—miRNAs, Genes and Interaction Networks

Cited by 104 publications

References 15 publications

cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

Exosomal miR-92a Concentration in the Serum of Shift Workers

Identification of regulatory microRNAs for hypoxia induced coagulation mechanism byIn-silicoanalysis

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