MicroRNAs (miRNAs) are a novel class of gene regulators that are now the center of their own research field in human cancer: the non-coding RNA field. MiRNAs are ~22nt long non-coding RNA transcripts that derive from hairpin precursors and regulate gene-expression of target genes by inhibiting the protein production of the target genes’ messenger RNA (Jonas and Izaurralde 2015; Lin and Gregory 2015). Although much is known about miRNAs, with now nearly 40’000 scientific articles written about them alone, paradoxically defining what is and what is not a miRNA has been difficult, severely hampering studies on their potential roles in cancer, for example.
In order to enable researchers to accurately study the dynamics of the human miRNA landscape, an international group under the lead of Professor Kevin J. Peterson (Dartmouth, US) and Dr. Bastian Fromm (Oslo, Norway) decided to revisit the available human miRNA complement (Kozomara and Griffiths-Jones 2014). Fromm et al established and then applied a set of consistent criteria for the annotation of miRNAs. This set was derived from numerous recent publications that elucidated details of miRNA maturation/processing in the cell (Auyeung, et al. 2013; Schirle and MacRae 2012; Schirle, et al. 2014a; Schirle, et al. 2014b; Seitz, et al. 2008; Suzuki, et al. 2015; Tsutsumi, et al. 2011). They show that less than a third of the 1,881 human miRBase entries are robustly supported as the products of miRNA genes. These robustly supported 523 human miRNA genes sequences are [click to continue…]
The organizers are happy to announce the upcoming “NGS and non-coding RNA data analysis” workshop II (2014) 15-16 May, Plovdiv, Bulgaria
The SeqAhead COST action BM1006 is organizing a 2 day workshop with presentations on non-coding RNA (ncRNA) research, bioinformatics, data analysis and stimulating discussions between biologists and bioinformaticians. The registration for this COST WS is now open.
The Workshop will concentrate on current topics in NGS and non-coding RNAs, with special emphasis on data analysis. The ultimate goal of the workshop is to bring software developers, bioinformaticians and experimental scientists together, bridging the gap between users’ needs and developers’ goals.
-biologists with research in ncRNA (ncRNA, small RNAs, miRNAs) applying or planning to apply Next Generation Sequencing technologies
-bioinformaticians involved in data analysis or developing algorithms for data analysis of ncRNA data.
The workshop is open for everybody in the ncRNA and NGS field. The workshop is free of charge and participants have to pay their own hotel and travel. COST will offer travel reimbursement to some selected researchers and you will need to provide a poster abstract.
For more detailed information visit the WS homepage:
Researchers at the University of Oxford and the Scripps Research Institute recently published an article evaluating the use of several different RT-qPCR normalization strategies when profiling miRNA gene expression in mouse serum. In their research article entitled “Assessment of RT-qPCR Normalization Strategies for Accurate Quantification of Extracellular microRNAs in Murine Serum,” Roberts et. al. compare three miRNA expression normalization strategies: 1.) normalization of miRNA expression to the average Cq (Ct) of all measured miRNA genes, 2.) Normalization of gene expression to individual miRNAs such as miR-16, miR-223, or miR-31 (all miRNA genes previously identified as normalization controls in the literature), and 3.) Normalization to a ‘spike-in’ external control miRNA gene expressed in C. elegans (cel-miR-39).
Normalization strategies have been an increasingly important topic in miRNA expression studies. This is especially true when profiling miRNA expression in serum or tissues and when quantifying miRNA genes which can have considerable variability in their endogenous expression. The authors identified a panel of 124 serum miRNA genes present in all their samples between normal, dystrophic, and dystrophic-treated mice. Their results suggest that [click to continue…]
StarBase has been updated to explore Pan-Cancer pattern of lncRNAs, miRNAs, RNA-binding proteins (RBP) and their regulatory networks (ceRNA, coexpression) by mining expression profiles of miRNAs, lncRNAs and mRNAs across 14 cancer types (>6000 samples) from The Cancer Genome Atlas (TCGA) Data Portal (all data available without limitations).
StarBase provides the following Pan-Cancer Analysis Services:
starBase constructed Pan-Cancer expression profiles of lncRNAs, miRNAs from TCGA RNA-Seq and miRNA-Seq data.
starBase generated Pan-Cancer networks of CLIP-Seq experimentally supported miRNA-lncRNA and miRNA-mRNA interactions.
starBase identified Pan-Cancer ceRNA networks involving lncRNAs and mRNAs by analyzing >6000 tumor and normal samples and [click to continue…]
MONMOUTH JUNCTION, NJ–(Marketwired – January 02, 2014) - DiamiR, LLC, a molecular diagnostics company focused on the development and commercialization of innovative blood-based tests for detection and monitoring of neurodegenerative diseases and cancer, announced today the publication entitled “Plasma microRNA biomarkers for detection of mild cognitive impairment: biomarker validation study” in Aging. Mild Cognitive Impairment is a […]
COLUMBUS, Ohio, and NEW YORK, Sept. 26, 2013 /PRNewswire/ – The Ohio State University today announced the signing of an exclusive world-wide agreement with Microlin Bio Inc., licensing a large portfolio of Ohio State’s groundbreaking cancer discoveries. The portfolio includes nearly 100 issued and pending microRNA patents that could lead to entirely new, more effective and more targeted ways to diagnose and treat […]
starBase v2.0 update available starBase is a database that can be used for decoding miRNA-mRNA, miRNA-ceRNA, miRNA-lncRNA, miRNA-circRNA, miRNA-pseudogene and protein-RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. starBase v2.0 now also provides visualization, analysis, discovery and downloading of above-mentioned large-scale functional genomics data. Currently, starBase v.20 includes (1)108 CLIP-Seq datasets, (2)~500,000 miRNA-mRNA […]
September 18, 2013 / B3C newswire / - Major new funding for research into epilepsy is announced today. The EpimiRNA Consortium, involving 16 partners from 8 European countries, the USA and Brazil has received €11.5 million funding from the European Union’s Framework Programme 7 to investigate molecular mechanisms, diagnostics and treatments for epilepsy. Over 50 million people […]
Demonstrating Increased Demand for the Rosetta Cancer Origin Test PRINCETON, NJ and REHOVOT, ISRAEL–(Marketwired – Sep 10, 2013) – Rosetta Genomics, Ltd. (NASDAQ: ROSG), a leading developer of microRNA-based molecular diagnostics, today reports financial results for the six months ended June 30, 2013. Commercial highlights for the first half of 2013 and recent weeks include: Enhanced […]