Genomics

Dataset Information

0

Validation of human microRNA target pathways enables evaluation of target prediction tools [miRNA]


ABSTRACT: MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome but that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool MIRTAH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson’s Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.

ORGANISM(S): Homo sapiens

PROVIDER: GSE135149 | GEO | 2020/11/13

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2020-11-13 | GSE135150 | GEO
2017-03-08 | GSE89156 | GEO
2016-10-01 | GSE84971 | GEO
2021-09-08 | PXD013987 | Pride
2013-06-08 | E-GEOD-47737 | biostudies-arrayexpress
2020-10-23 | GSE159200 | GEO
2021-03-08 | GSE133775 | GEO
2019-10-14 | PXD015278 | Pride
2020-09-01 | GSE103349 | GEO
2018-03-29 | GSE103473 | GEO