ArticleBMC research notes2014
Analysis options for high-throughput sequencing in miRNA expression profiling.
Article in BMC research notes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
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Who cites it
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Circulating Levels of microRNA-122 and Hepatic Fat Change in Response to Weight-Loss Interventions: CENTRAL Trial.The Journal of clinical endocrinology and metabolism · 2022Trial
- The role of microRNAs on autophagy in cervical cancer: review.Discover oncology · 2025Review
- MicroRNAs in Plant Genetic Regulation of Drought Tolerance and Their Function in Enhancing Stress Adaptation.Plants (Basel, Switzerland) · 2025Review
- Extracellular vesicles from highly invasive melanoma subpopulations increase the invasive capacity of less invasive melanoma cells through mir-1246-mediated inhibition of CCNG2.Cell communication and signaling : CCS · 2024Article
- Blood miRNAs miR-549a, miR-552, and miR-592 serve as potential disease-specific panels to diagnose colorectal cancer.Heliyon · 2024Article
- Insights Into Colorectal Carcinoma: A Comprehensive Review of MicroRNA Expression Patterns.Cureus · 2024Review
- Review
- Data Normalization of Urine miRNA Profiling from Head and Neck Cancer Patients Treated with Cisplatin.International journal of molecular sciences · 2023Article
- Clonal Hematopoiesis Mutations Are Present in Atherosclerotic Lesions in Peripheral Artery Disease.International journal of molecular sciences · 2023Article
- Analysis of genomic alterations in cancer associated human pancreatic stellate cells.Scientific reports · 2022Article
- Dysregulation of MiR-144-5p/RNF187 Axis Contributes To the Progression of Colorectal Cancer.Journal of translational internal medicine · 2022Article
- STAT3 Enhances Sensitivity of Glioblastoma to Drug-Induced Autophagy-Dependent Cell Death.Cancers · 2022Article
- The Network of miRNA-mRNA Interactions in Circulating T Cells of Patients Following Major Trauma - A Pilot Study.Journal of inflammation research · 2022Article
- Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches ofFrontiers in plant science · 2022Article
- Comprehensive Analyses of miRNAs Revealed miR-92b-3p, miR-182-5p and miR-183-5p as Potential Novel Biomarkers in Melanoma-Derived Extracellular Vesicles.Frontiers in oncology · 2022Article
- Improving one-step scarless genome editing inBiology methods & protocols · 2022Article
- MiRNA Deregulation Distinguishes Anaplastic Thyroid Carcinoma (ATC) and Supports Upregulation of Oncogene Expression.Cancers · 2021Article
- The MicroRNA Landscape of MYCN-Amplified Neuroblastoma.Frontiers in oncology · 2021Article
- Differential MicroRNA-Signatures in Thyroid Cancer Subtypes.Journal of oncology · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling.Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression.
methodsWe compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors.
resultsHigh correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers.
conclusionsCompared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail.
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