miRWalk: An online resource for prediction of microRNA binding sites

Sticht, Carsten; Torre, Carolina De La; Parveen, Alisha; Gretz, Norbert

doi:10.1371/journal.pone.0206239

Cited by 1,275 publications

(1,063 citation statements)

References 8 publications

(8 reference statements)

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“…In agreement with these observations, we found significantly reduced Nefl protein expression in the ENS. In addition, we observed significant upregulation of miRNAs that regulate Nefl, such as let-7i-5p, miR-10a-5p, miR-22-3p, miR-23a, miR-30c-5p, miR-99a-5p, miR-125a-5p, miR-126a-5p, miR-126b-5p, and miR-181a-5p 68,69 . Globular and filamentous actins are highly enriched in dendritic spines and are ABPs, such as profilin and the actin-related-protein 2/3 complex (Arpc4), control actin polymerization and are dysregulated in brain disorders such as Alzheimer's disease and schizophrenia as well as in neurodevelopmental disorders such as autism 70,71,72 .…”

Section: Discussionmentioning

confidence: 86%

“…Significant changes in expression were observed in miRNAs that target Nefl, Vamp2, and Calb2, supporting our idea that these proteins are potential biomarkers for early-stage PD. Detailed examination of protein-miRNA clustering using mirWALK 3.0 (Sticht et al, 2018) revealed that Nefl is targeted by let 7i-5p, miR-10a-5p, miR-22-3p, miR-23a-3p, miR-30c-5p, miR-99a-5p, miR-125a-5p, miR-126-3p, miR-126-5p, and miR-181a-5p ( Fig. 5d, pink framed boxes); and Vamp2 is targeted by let-7i-5p, miR-10a-5p, miR-22-3p, miR-30c-5p, miR-99a-5p, miR-135a-5p, miR-338-3p, miR-350-3p, miR-377-3p, and miR-495-3p ( Fig.…”

Section: Dysregulated Mirna Expression In the Ens Of Psa30p Micementioning

confidence: 99%

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Functional and molecular early enteric biomarkers for Parkinson’s disease in mice and men

Gries

Christmann

Schulte

et al. 2020

Preprint

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Parkinson's disease (PD) usually has a late clinical onset. The lack of early biomarkers for the disease represents a major challenge for developing timely treatment interventions. Here, we use an -synuclein-overexpressing transgenic (Th-1-SNCA-A30P) mouse model of PD to identify appropriate candidate markers in the gut for early stages of PD before hallmark symptoms begin to manifest. A30P mice did not show alterations in gait parameters at 2 months of age, and these mice were therefore defined as pre-symptomatic A30P mice (psA30P). We discovered early functional motility changes in the gut and early molecular dysregulations in the myenteric plexus of psA30P mice by comparative protein and miRNA profiling and cell culture experiments. We found that the proteins neurofilament light chain, vesicle-associated membrane protein 2 and calbindin 2, together with the miRNAs that regulate them, are potential biomarkers of early PD that may facilitate timely treatment and/or prevention of PD in men.

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Section: Discussionmentioning

confidence: 86%

Section: Dysregulated Mirna Expression In the Ens Of Psa30p Micementioning

confidence: 99%

Functional and molecular early enteric biomarkers for Parkinson’s disease in mice and men

Gries

Christmann

Schulte

et al. 2020

Preprint

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“…Therefore, these SNPs might affect the corresponding phenotypic trait in sheep, possibly by disrupting miRNA binding as in the myostatin example from Texel sheep described in [74]. Further analysis using the miRWalk database [75] predicted that one of the SNPs on chromosome 16 (31362143 bp) that exhibited allelic expression imbalance is located within a microRNA binding site, in the 3’ UTR of CCL28 . Interestingly, the same microRNA (bta-mir-29e) in dairy cattle has been already reported to be differentially expressed in bovine mastitis caused by gram positive bacteria [76].…”

Section: Discussionmentioning

confidence: 99%

Genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep

Banos

Clark

Bush

et al. 2019

Preprint

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24Milk yield is the most important dairy sheep trait and constitutes the key genetic improvement 25 goal via selective breeding. Mastitis is one of the most prevalent diseases, significantly 65 Page4 66Beyond simply increasing milk production, the dairy sheep industry faces challenges such as 67 the need to offer healthy products to consumers, addressing animal welfare, and ensuring the 68 long-term competitiveness and sustainability of the sector. Mastitis is the most prevalent and 69 costly disease in the dairy industry due to reduced and discarded milk, early involuntary culling 70 of animals, and veterinary services and labour costs [6, 7]. The disease also poses a potential 71 threat of zoonosis and antimicrobial resistance if antibiotic treatment is not applied carefully 72 [6][7][8]. Moreover, mastitis is a welfare concern because of associated pain, anxiety and 73 restlessness, and upsets the normal feeding behaviour of the animals [9]. Host resistance to 74 mastitis is a moderately heritable trait [7]. Recently, an ovine custom made mastitis specific 75 960-SNP DNA array was built to facilitate genetic selection and improvement of animal 76 resistance to mastitis in dairy sheep [10] [11] [12] [13]. We previously used this array in a 77 genomic association study and detected five quantitative trait loci (QTLs) for mastitis 78 resistance in Chios sheep [10]. 80In the present study, we examined the genetic and genomic relationship between milk yield 81 and mastitis resistance in the Chios sheep, using pedigree and genomic information. The 82 relationship between the two traits is crucial if mastitis resistance is to be included in selective 83 breeding goals together with increased milk yield. We estimated genetic parameters and 84 investigated whether relevant QTLs for milk yield exist in previously identified mastitis-85 specific genomic regions. We also performed pathway analysis and examined gene expression 86 and allelic expression imbalance to characterise the genes located under the QTL regions in 87 relation with milk yield and mastitis resistance. 88 Page5 89 Materials and Methods 90 91 Ethical statement 92 The study was approved by the Ethics and Research Committee of the Faculty of Veterinary 93 Medicine, Aristotle University of Thessaloniki, Greece. Permits for access and use of the 94 commercial farms were granted by the farm owners, who were members of the Chios Sheep 95 Breeders' Cooperative "Macedonia". During sampling, animals were handled by qualified 96 veterinarians. Permission to qualified veterinarians to perform milk and blood sampling was 97 granted by the National (Greek) Legislature for the Veterinary Profession, No. 344/29-12-98 2000. 99 100 Animals, sampling and phenotyping 101 Animals used in the present study included 609 purebred Chios dairy ewes raised in four 102 commercial farms in Greece. Complete pedigree data were available for these animals. Ewes 103 were in their first or second lactation. Daily milk yield was recorded on each animal on the day 104 of monthly visits t...

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“…TargetScan (13), miRWalK (14), miRBase (15) and miRTarBase (16) all allows for miRNA target prediction. The union set was used to miRNA-mRNA network construction.…”

Section: Target Gene Prediction Of Mirnamentioning

confidence: 99%

Complement C3 as therapeutic target in diabetic nephropathy by bioinformatics analysis

Tang

Wang²,

Deng³

et al. 2020

Preprint

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Background: Various public platforms have contained extensive data for deeper bioinformatics analysis. The pathogenesis of diabetic nephropathy is always a hot topic and the underlying molecular events are not completely clear.Methods: Differential expression analysis and weighted correlation network analysis (WGCNA) were applied to screen meaningful gene in GSE30529. The combined result was used for gene ontology (GO) annotation and KEGG pathway enrichment analysis. STRING was used for protein-protein interaction (PPI) network construction and Cytoscape software was used for hub gene identification.Gene methylation profile GSE121820 and miRNA profile GSE51674 were also acquired to perform multi-omics analysis. Clinical features were obtained form Nephroseq and potential drugs were identified by CMap.Results: 345 genes were obtained form GSE30529 after differential expression analysis and WGCNA.GO analysis mainly included neutrophil activation, regulation of immune effector process, positive regulation of cytokine production and neutrophil mediated immunity. KEGG pathway analysis mostly included phagosome, complement and coagulation cascades, cell adhesion molecules and AGE-RAGE signaling pathway in diabetic complications. 16 down regulated miRNAs were obtained from GSE57674 to construct miRNA-mRNA network. Top 20 genes were discerned from PPI network and there were DNA methylation differences in 15 genes among them. Correlation analysis showed SYK, CXCL1, LYN, VWF, ANXA1, C3, HLA-E, RHOA, SERPING1, EGF and KNG1 may involved in DN. 10 small molecule compounds have been identified as potential therapeutic drugs.Conclusion: We screened 11 target genes and suggested C3 may serve as a therapeutic target in diabetic nephropathy.

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miRWalk: An online resource for prediction of microRNA binding sites

Cited by 1,275 publications

References 8 publications

Functional and molecular early enteric biomarkers for Parkinson’s disease in mice and men

Functional and molecular early enteric biomarkers for Parkinson’s disease in mice and men

Genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep

Complement C3 as therapeutic target in diabetic nephropathy by bioinformatics analysis

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