Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma
Johannes H. Schulte,Tobias Marschall,Marcel Martin,Philipp Rosenstiel,Pieter Mestdagh,Stefanie Schlierf,Theresa Thor,Jo Vandesompele,Angelika Eggert,Stefan Schreiber,Sven Rahmann,Alexander Schramm +11 more
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TLDR
In this paper, the authors analyzed the small RNA transcriptomes of five favorable and five unfavorable NBs using SOLiD next-generation sequencing, generating a total of >188 000 000 reads.Abstract:
Small non-coding RNAs, in particular microRNAs(miRNAs), regulate fine-tuning of gene expression and can act as oncogenes or tumor suppressor genes. Differential miRNA expression has been reported to be of functional relevance for tumor biology. Using next-generation sequencing, the unbiased and absolute quantification of the small RNA transcriptome is now feasible. Neuroblastoma(NB) is an embryonal tumor with highly variable clinical course. We analyzed the small RNA transcriptomes of five favorable and five unfavorable NBs using SOLiD next-generation sequencing, generating a total of >188 000 000 reads. MiRNA expression profiles obtained by deep sequencing correlated well with real-time PCR data. Cluster analysis differentiated between favorable and unfavorable NBs, and the miRNA transcriptomes of these two groups were significantly different. Oncogenic miRNAs of the miR17-92 cluster and the miR-181 family were overexpressed in unfavorable NBs. In contrast, the putative tumor suppressive microRNAs, miR-542-5p and miR-628, were expressed in favorable NBs and virtually absent in unfavorable NBs. In-depth sequence analysis revealed extensive post-transcriptional miRNA editing. Of 13 identified novel miRNAs, three were further analyzed, and expression could be confirmed in a cohort of 70 NBs.read more
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MicroRNA Molecular Profiles Associated with Diagnosis, Clinicopathologic Criteria, and Overall Survival in Patients with Resectable Pancreatic Ductal Adenocarcinoma
Nigel B. Jamieson,Douglas C. Morran,Jennifer P. Morton,Asif Ali,Euan J. Dickson,C. Ross Carter,Owen J. Sansom,T.R. Jeffry Evans,Colin J. McKay,Karin A. Oien +9 more
TL;DR: In this article, the relationship between miRNA expression and clinicopathologic parameters, including prognosis, in pancreatic ductal adenocarcinoma (PDAC) was investigated.
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Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
Shu-Jen Chen,Gian-Hung Chen,Yi-Hsuan Chen,Cheng-Yuan Liu,Kai-Ping Chang,Yu-Sun Chang,Hua-Chien Chen +6 more
TL;DR: Analysis of Epstein-Barr virus genomic sequences indicated that the majority of EBV miRNA nucleotide variants resulted from post-transcriptional modifications, suggesting that seed sequence content may be an important factor underlying the differential accumulation of BART miRNAs.
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RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing
Henrike Maatz,Marvin Jens,Martin Liss,Sebastian Schafer,Matthias Heinig,Marieluise Kirchner,Eleonora Adami,Carola Rintisch,Vita Dauksaite,Michael H. Radke,Matthias Selbach,Paul J.R. Barton,Stuart A. Cook,Nikolaus Rajewsky,Michael Gotthardt,Markus Landthaler,Norbert Hubner +16 more
TL;DR: Combined transcriptome-wide crosslinking immunoprecipitation, RNA-seq, and quantitative proteomics analyses identify RBM20-regulated targets and provide insight into the pathogenesis of human heart failure.
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Molecular diagnosis and therapy of hepatocellular carcinoma (HCC): An emerging field for advanced technologies
TL;DR: This review aims to summarize recent progress of system biological approaches in hepatocarcinogenesis and outline potential areas for translational application in a clinical setting and indicate ongoing experimental research utilizing novel technologies in diagnosis and treatment of this deadly disease.
Book ChapterDOI
miRNA expression profiling: from reference genes to global mean normalization.
TL;DR: The power of the previously described global meannormalization method is summarized in comparison to the multiple reference gene normalization method using the most stably expressed small RNA controls and a modified global mean normalization strategy based on the attribution of equal weight to each individual miRNA during normalization is compared.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
MicroRNAs: Genomics, Biogenesis, Mechanism, and Function
TL;DR: Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.
Journal ArticleDOI
The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
Stephen A. Bustin,Vladimir Benes,Jeremy A. Garson,Jan Hellemans,Jim F. Huggett,Mikael Kubista,Reinhold Mueller,Tania Nolan,Michael W. Pfaffl,Gregory L. Shipley,Jo Vandesompele,Carl T. Wittwer,Carl T. Wittwer +12 more
TL;DR: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency.
Journal Article
Oncomirs : microRNAs with a role in cancer
TL;DR: I MicroRNAs (miRNAs) are an abundant class of small non-protein-coding RNAs that function as negative gene regulators as discussed by the authors, and have been shown to repress the expression of important cancer-related genes and might prove useful in the diagnosis and treatment of cancer.
Journal ArticleDOI
A direct approach to false discovery rates
TL;DR: The calculation of the q‐value is discussed, the pFDR analogue of the p‐value, which eliminates the need to set the error rate beforehand as is traditionally done, and can yield an increase of over eight times in power compared with the Benjamini–Hochberg FDR method.
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