qPCR NEWS - July 2012 - focus on microRNA

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qPCR NEWS - July 2012 - focus on microRNA ---------------------------------------------------------- Dear researcher, dear Gene Quantification page reader, Our newsletter informs about the latest news in quantitative real-time PCR = (qPCR and RT-qPCR), which are compiled and summarised on the=20 Gene Quantification homepage. The focus of this newsletter issue is: * Update on integrated analysis of microRNA and mRNA expression - http://in= tegrated-analysis.Gene-Quantification.info * Update of new microRNA reviews and interesting microRNA normalisation pap= ers - http://microRNA.Gene-Quantification.info * Second announcement qPCR & NGS Symposium in March 2013 - http://www.qPCR-= NGS-2013.net=20 * GenEx - a powerful tool For qPCR data analysis - download a free trial ve= rsion - http://GenEx.gene-quantification.info ---------------------------------------------------------------------------= -- If this newsletter is not displayed correctly by your email client, please= use following http://qPCRnews.gene-quantification.info ---------------------------------------------------------------------------= -- Quantification of miRNA-mRNA interactions Muniategui A, Nogales-Cadenas R, V=C3=A1zquez M, L Aranguren X, Agirre X, L= uttun A, Prosper F, Pascual-Montano A, Rubio A. Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebast= ian, Spain. PLoS One. 2012;7(2):e30766. Epub 2012 Feb 14. There is also a web-based tool for human miRNAs at http://talasso.cnb.csic.= es miRNAs are small RNA molecules (' 22nt) that interact with their correspond= ing target mRNAs inhibiting the translation of the mRNA into proteins and c= leaving the target mRNA. This second effect diminishes the overall expressi= on of the target mRNA. Several miRNA-mRNA relationship databases have been = deployed, most of them based on sequence complementarities. However, the nu= mber of false positives in these databases is large and they do not overlap= completely. Recently, it has been proposed to combine expression measureme= nt from both miRNA and mRNA and sequence based predictions to achieve more = accurate relationships. In our work, we use LASSO regression with non-posit= ive constraints to integrate both sources of information. LASSO enforces th= e sparseness of the solution and the non-positive constraints restrict the = search of miRNA targets to those with down-regulation effects on the mRNA e= xpression. We named this method TaLasso (miRNA-Target LASSO).We used TaLass= o on two public datasets that have paired expression levels of human miRNAs= and mRNAs. The top ranked interactions recovered by TaLasso are especially= enriched (more than using any other algorithm) in experimentally validated= targets. The functions of the genes with mRNA transcripts in the top-ranke= d interactions are meaningful. This is not the case using other algorithms.= TaLasso is available as Matlab or R code. There is also a web-based tool fo= r human miRNAs at http://talasso.cnb.csic.es ---------------------------------------------------------------------------= ----- Joint analysis of miRNA and mRNA expression data Muniategui A, Pey J, Planes F, Rubio A. Brief Bioinform. 2012 Jun 12. miRNAs are small RNA molecules ('22=E2=80=89nt) that interact with their ta= rget mRNAs inhibiting translation or/and cleavaging the target mRNA. This i= nteraction is guided by sequence complentarity and results in the reduction= of mRNA and/or protein levels. miRNAs are involved in key biological proce= sses and different diseases. Therefore, deciphering miRNA targets is crucia= l for diagnostics and therapeutics. However, miRNA regulatory mechanisms ar= e complex and there is still no high-throughput and low-cost miRNA target s= creening technique. In recent years, several computational methods based on= sequence complementarity of the miRNA and the mRNAs have been developed. H= owever, the predicted interactions using these computational methods are in= consistent and the expected false positive rates are still large. Recently,= it has been proposed to use the expression values of miRNAs and mRNAs (and= /or proteins) to refine the results of sequence-based putative targets for = a particular experiment. These methods have shown to be effective identifyi= ng the most prominent interactions from the databases of putative targets. = Here, we review these methods that combine both expression and sequence-bas= ed putative targets to predict miRNA targets. More papers about the integrated analysis of microRNA and mRNA expression = =3D> http://integrated-analysis.Gene-Quantification.info ---------------------------------------------------------------------------= -- New microRNA reviews Technology features, pitfalls and recommendations for microRNA expression p= rofiling http://microRNA.Gene-Quantification.info - MicroRNA profiling: approaches and considerations - The widespread regulation of microRNA biogenesis, function and decay - Strengths and limitations of laboratory procedures for microRNA detection - Editorial - Studying microRNAs in the brain: technical lessons learned fr= om the first ten years - Pitfalls and recommendations for microRNA expression analysis using qPCR - Potential pitfalls in microRNA profiling - Technolgy Feature - MicroRNA profiling: separating signal from noise - How Do MicroRNAs Regulate Gene Expression? - Normalization strategies for microRNA profiling experiments: a 'normal' w= ay to a hidden layer of complexity? - The microcosmos of cancer - miRNAs in human cancer ---------------------------------------------------------------------------= -- New interesting microRNA normalisation papers http://microRNA.Gene-Quantification.info - Overview and workflow in microRNA normalisation - Whole-Genome RT-qPCR MicroRNA Expression Profiling - Profound Effect of Profiling Platform and Normalization Strategy on Detec= tion of Differentially Expressed MicroRNAs - A Comparative Study - Identification of reference microRNAs and suitability of archived hemopoi= etic samples for robust microRNA expression profiling - Identification of suitable reference genes for qPCR analysis of serum mic= roRNA in gastric cancer patients - Suitable reference genes for relative quantification of miRNA expression = in prostate cancer - Comprehensive human adipose tissue mRNA and microRNA endogenous control s= election for quantitative real-time-PCR normalization - MicroRNA expression profiling to identify and validate reference genes fo= r relative quantification in colorectal cancer - miRNA expression profiling - from reference genes to global mean normaliz= ation - Identification by Real-time PCR of 13 mature microRNAs differentially exp= ressed in colorectal cancer and non-tumoral tissues - Expression profiling of microRNA using real-time quantitative PCR, how to= use it and what is available - A novel and universal method for microRNA RT-qPCR data normalization ---------------------------------------------------------------------------= -- Second announcement qPCR & NGS Symposium in Freising-Weihenstephan 18-22 March 2013 http://www.qPCR-NGS-2013.net Download the latest Event Flyer =3D> http://tinyurl.com/qPCR-NGS-2013 On behalf of the Organisation Committee and the Scientific Board it is a gr= eat pleasure to invite you to the 6th International qPCR & NGS 2013 Event. = The event is divided in a 3-day scientific Symposium with an Industrial Exh= ibition and various 2-day Application Workshop to be held at the Center of = Life Science in Freising Weihenstephan, Technische Universit=C3=A4t M=C3=BC= nchen (Germany). The great international interest in the previous meetings = ( qPCR 2004 to qPCR 2011 ) led us to the decision to repeat the Symposium i= n spring 2013. We expect 500-600 participants coming from all over the worl= d, in 2011 we could welcome participants from 56 contries, and roughly 30-4= 0 international companies in the qPCR Industrial Exhibition. We have set the date for the qPCR & NGS 2013 Event to 18th - 22nd March 201= 3. The event location is the central lecture hall complex and the foyer at = TUM (Technical University of Munich) in Freising Weihenstephan, Germany (Go= ogle Maps link or Google Earth link). The TUM and the Biotech region around= Munich is part of the largest Biotech cluster in Europe, located close to = the Munich airport in the heart of Bavaria. The focus of the qPCR & NGS 2013 Event will be on: Next Generation Thinki= ng in Molecular Diagnostics Leading academic researchers and industrial contributors in the field will = participate in the symposium, which will be an arena for fruitful discussio= ns between researchers of different backgrounds. The Symposium Talks, Poste= r Sessions, Industrial Exhibition and associated qPCR & NGS Application Wor= kshops offer an overview of the present knowledge and future developments i= n qPCR, next generation sequencing and gene expression measurement technolo= gy and its wide applications in research. The symposium will focus on 70 lectures and a huge poster exhibition will b= e presented by internationally recognised experts in their field. The empha= sis will be on unbiased, didactic information exchange. Internationally ren= own speakers will be participating in a lively and exciting programme enabl= ing the valuable exchange of information in the qPCR and Next Generation Se= quencing field. One third of the talks will be presented by selected invite= d speakers, one third will be selected from the submitted abstracts and one= third will be presented by qPCR & NGS related company R&D representatives.= All scientific contributions will be published in the Symposium Proceeding= s (ISBN to be announced). Full papers from selected invited academic and industrial speakers and appl= ication notes from industrial speakers will be published in a METHODS speci= al issue =E2=80=9CTranscriptional Biomarkers=E2=80=9D edited by Michael W.= Pfaffl (published January 2013). At the meeting all participants will get= a free hard cover of this special Methods issue. Please have a look to ou= r previous issue =3D> =E2=80=9CThe ongoing evolution of qPCR=E2=80=9D METH= ODS special qPCR Vol 50 issue 4 (April 2010) Please register using the Internet based ConfTool registration and submissi= on platform =3D> http://registration.qPCR-NGS-2013.net ---------------------------------------------------------------------------= -- Symposium Talk and Poster sessions: http://sessions.qpcr-ngs-2013.net/ - Main Topic: Molecular diagnostics - Main Topic: Next Generation Sequencing (NGS) - Main Topic: Transcriptional Biomarkers - High throughput analysis in qPCR - Systems biology - Single-cells diagnostics - MIQE & QM strategies in qPCR - non-coding RNAs - microRNA, siRNA, long non-coding RNAs - Digital PCR & Nano-fluidics - Pre-analytical Steps - BioStatistics & BioInformatics - qPCR & NGS data analysis - Lunch Seminars: - qBASEplus - data analysis lunch seminar - GenEx - data analysis lunch seminar - NGS data analysis lunch seminars - more to be announced........ View our qPCR 2011 event trailer on YouTube =3D> http://www.youtube.com/wat= ch?v=3Dcp8WwPyLW8Y Download the latest Event Flyer =3D> http://tinyurl.com/qPCR-NGS-2013 Please register using the Internet based ConfTool registration and submissi= on platform =3D> http://registration.qPCR-NGS-2013.net ---------------------------------------------------------------------------= -- GenEx 5 - A Powerful Tool For qPCR Data Analysis Download a free trail version here =3D> http://GenEx.gene-quantification.in= fo GenEx is a popular software for qPCR data processing and analysis. Built in= a modular fashion GenEx provides a multitude of functionalities for the qP= CR community, ranging from basic data editing and management to advanced cu= tting-edge data analysis. View our webpage =3D> http://GenEx.gene-quantific= ation.info Basic data editing and management Arguably the most important part of qPCR experiments is to pre-process the = raw data into shape for subsequent statistical analyses. The pre-processing= steps need to be performed consistently in correct order and with confiden= ce. GenEx Standard=E2=80=99s streamlined and user-friendly interface ensure= s mistake-free data handling. Intuitive and powerful presentation tools all= ow professional illustrations of even the most complex experimental designs= .. Advanced cutting-edge data analysis When you need more advanced analyses GenEx Enterprise is the product for yo= u. Powerful enough to demonstrate feasibility it often proves sufficient fo= r most users demands. Current features include parametric and non-parametri= c statistical tests, Principal Component Analysis, and Artificial Neural Ne= tworks. New features are continuously added to GenEx with close attention t= o customers=E2=80=99 needs. New features Sample handling and samples individual biology often contribute to confound= ing experimental variability. By using the new nested ANOVA feature in GenE= x version 5 user will be able to evaluate variance contributions from each = step in the experimental procedure. With a good knowledge of the variance c= ontributions, an appropriate distribution of experimental replicates can be= selected to minimize confounding variance and maximize the power of the ex= perimental design! For experiments with complex features, such as for examp= le multifactorial diseases, analytical relationships and classifications ma= y not readily be available. The support vector machine feature in the new v= ersion of GenEx is so easy to use that it will make this advanced supervise= d classification method easily available to novice users, while providing a= ccess to advanced parameters for experts. Download a free trail version here =3D> http://GenEx.gene-quantification.in= fo GenEx PDF user guides: * GenEx user guide=20 * GenEx user guide - Exiqon Wizard=20 * GenEx user guide - Roche Wizard ---------------------------------------------------------------------------= -- Please forward this qPCR NEWS http://api.addthis.com/oexchange/0.8/forward= /email/offer?url=3Dhttp://qPCRnews.gene-quantification.info&title=3DJoin+ou= r+monthly+newsletter+on&username=3DqPCR-NEWS&email_template=3D&lng=3Den-us = to further scientists and friends who are interested in qPCR ! Best regards, Michael W. Pfaffl responsible Editor of the Gene Quantification Pages ---------------------------------------------------------------------------= -- The qPCR NEWS and the Gene Quantification Pages are educational sites with = the only purpose of facilitating access to qPCR related information on the = internet. The qPCR NEWS and the Gene Quantification Pages are edited by Mic= hael W. Pfaffl. Copyright =C2=A92005-2012 All rights reserved. Any unauthorized use, reprod= uction, or transfer of this message or its contents, in any medium, is stri= ctly prohibited. Disclaimer & Copyrights are displayed on the homepage http= ://www.gene-quantification.info To subscribe or change your e-mail address in qPCR NEWS, and if you would l= ike to receive future issues FREE of charge, please send an e-mail with the= subject SUBSCRIBE mailto:newsletter@gene-quantification.info?subject=3DSUB= SCRIBE