 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 13, 2020 |
| Title |
Validation of human microRNA target pathways enables evaluation of target prediction tools [mRNA] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
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.
|
| |
|
| Overall design |
LUHMES cells were differentiated towards dopaminergic neurons and treated with the neurotoxin MPP+ to induce PD phenotype. Alterations in miRNome as well as transcriptome were measured by microarray in four independet experiments.
|
| |
|
| Contributor(s) |
Kern F, Krammes L, Danz K, Diener C, Kehl T, Küchler O, Fehlmann T, Kahraman M, Rheinheimer S, Aparicio E, Wagner S, Ludwig N, Backes C, Lenhof H, von Briesen H, Hart M, Keller A, Meese E |
| Citation(s) |
33305319 |
| Submission date |
Jul 31, 2019 |
| Last update date |
Jan 19, 2021 |
| Contact name |
Lena Krammes |
| E-mail(s) |
lena.krammes@uni-saarland.de
|
| Organization name |
Saarland University
|
| Department |
Institute for Human Genetics
|
| Street address |
Kirrbergerstraße
|
| City |
Homburg |
| ZIP/Postal code |
66421 |
| Country |
Germany |
| |
|
| Platforms (1) |
| GPL21185 |
Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray 039494 [Probe Name Version] |
|
| Samples (8)
|
|
| This SubSeries is part of SuperSeries: |
| GSE135151 |
Validation of human microRNA target pathways enables evaluation of target prediction tools |
|
| Relations |
| BioProject |
PRJNA557595 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135150_RAW.tar |
98.2 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...