qPCR NEWS - July 2012 - focus on microRNA

Editor www.Gene-Quantification.info via methods%40net.bio.net (by editor from gene-quantification.info)
Thu Jul 26 11:19:59 EST 2012

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 
Gene Quantification homepage. The focus of this newsletter issue is:

* Update on integrated analysis of microRNA and mRNA expression - http://integrated-analysis.Gene-Quantification.info
* Update of new microRNA reviews and interesting microRNA normalisation papers - http://microRNA.Gene-Quantification.info
* Second announcement qPCR & NGS Symposium in March 2013 - http://www.qPCR-NGS-2013.net 
* GenEx - a powerful tool For qPCR data analysis - download a free trial version  -  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, Vázquez M, L Aranguren X, Agirre X, Luttun A, Prosper F, Pascual-Montano A, Rubio A.
Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebastian, 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 corresponding target mRNAs inhibiting the translation of the mRNA into proteins and cleaving the target mRNA. This second effect diminishes the overall expression of the target mRNA. Several miRNA-mRNA relationship databases have been deployed, most of them based on sequence complementarities. However, the number of false positives in these databases is large and they do not overlap completely. Recently, it has been proposed to combine expression measurement from both miRNA and mRNA and sequence based predictions to achieve more accurate relationships. In our work, we use LASSO regression with non-positive constraints to integrate both sources of information. LASSO enforces the sparseness of the solution and the non-positive constraints restrict the search of miRNA targets to those with down-regulation effects on the mRNA expression. We named this method TaLasso (miRNA-Target LASSO).We used TaLasso 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-ranked 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 for 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 nt) that interact with their target mRNAs inhibiting translation or/and cleavaging the target mRNA. This interaction is guided by sequence complentarity and results in the reduction of mRNA and/or protein levels. miRNAs are involved in key biological processes and different diseases. Therefore, deciphering miRNA targets is crucial for diagnostics and therapeutics. However, miRNA regulatory mechanisms are complex and there is still no high-throughput and low-cost miRNA target screening technique. In recent years, several computational methods based on sequence complementarity of the miRNA and the mRNAs have been developed. However, the predicted interactions using these computational methods are inconsistent 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 identifying the most prominent interactions from the databases of putative targets. Here, we review these methods that combine both expression and sequence-based putative targets to predict miRNA targets.

More papers about the integrated analysis of microRNA and mRNA expression => http://integrated-analysis.Gene-Quantification.info


New microRNA reviews
Technology features, pitfalls and recommendations for microRNA expression profiling

- 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 from 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' way to a hidden layer of complexity?
- The microcosmos of cancer
- miRNAs in human cancer


New interesting microRNA normalisation papers

- Overview and workflow in microRNA normalisation
- Whole-Genome RT-qPCR MicroRNA Expression Profiling
- Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs - A Comparative Study
- Identification of reference microRNAs and suitability of archived hemopoietic samples for robust microRNA expression profiling
- Identification of suitable reference genes for qPCR analysis of serum microRNA 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 selection for quantitative real-time-PCR normalization
- MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer
- miRNA expression profiling - from reference genes to global mean normalization
- Identification by Real-time PCR of 13 mature microRNAs differentially expressed 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
Download the latest Event Flyer => http://tinyurl.com/qPCR-NGS-2013

On behalf of the Organisation Committee and the Scientific Board it is a great 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 Exhibition and various 2-day Application Workshop to be held at the Center of Life Science in Freising Weihenstephan, Technische Universität München (Germany). The great international interest in the previous meetings ( qPCR 2004 to qPCR 2011 ) led us to the decision to repeat the Symposium in spring 2013. We expect 500-600 participants coming from all over the world, in 2011 we could welcome participants from 56 contries, and roughly 30-40 international companies in the qPCR Industrial Exhibition.

We have set the date for the qPCR & NGS 2013 Event to 18th - 22nd March 2013. The event location is the central lecture hall complex and the foyer at TUM (Technical University of Munich) in Freising Weihenstephan, Germany (Google 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 Thinking in Molecular Diagnostics

Leading academic researchers and industrial contributors in the field will participate in the symposium, which will be an arena for fruitful discussions between researchers of different backgrounds. The Symposium Talks, Poster Sessions, Industrial Exhibition and associated qPCR & NGS Application Workshops offer an overview of the present knowledge and future developments in qPCR, next generation sequencing and gene expression measurement technology and its wide applications in research.

The symposium will focus on 70 lectures and a huge poster exhibition will be presented by internationally recognised experts in their field. The emphasis will be on unbiased, didactic information exchange. Internationally renown speakers will be participating in a lively and exciting programme enabling the valuable exchange of information in the qPCR and Next Generation Sequencing field. One third of the talks will be presented by selected invited 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 Proceedings (ISBN to be announced).

Full papers from selected invited academic and industrial speakers and application notes from industrial speakers will be published in a METHODS special issue “Transcriptional Biomarkers”  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 our previous issue  => “The ongoing evolution of qPCR” METHODS special qPCR Vol 50 issue 4  (April 2010)

Please register using the Internet based ConfTool registration and submission platform => http://registration.qPCR-NGS-2013.net


Symposium Talk and Poster sessions:

- 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 => http://www.youtube.com/watch?v=cp8WwPyLW8Y

Download the latest Event Flyer => http://tinyurl.com/qPCR-NGS-2013

Please register using the Internet based ConfTool registration and submission platform => http://registration.qPCR-NGS-2013.net


GenEx 5 -  A Powerful Tool For qPCR Data Analysis
Download a free trail version here => http://GenEx.gene-quantification.info

GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis. View our webpage => http://GenEx.gene-quantification.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 confidence. GenEx Standard’s streamlined and user-friendly interface ensures mistake-free data handling. Intuitive and powerful presentation tools allow 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 you. Powerful enough to demonstrate feasibility it often proves sufficient for most users demands. Current features include parametric and non-parametric statistical tests, Principal Component Analysis, and Artificial Neural Networks. New features are continuously added to GenEx with close attention to customers’ needs.

New features
Sample handling and samples individual biology often contribute to confounding experimental variability. By using the new nested ANOVA feature in GenEx version 5 user will be able to evaluate variance contributions from each step in the experimental procedure. With a good knowledge of the variance contributions, an appropriate distribution of experimental replicates can be selected to minimize confounding variance and maximize the power of the experimental design! For experiments with complex features, such as for example multifactorial diseases, analytical relationships and classifications may not readily be available. The support vector machine feature in the new version of GenEx is so easy to use that it will make this advanced supervised classification method easily available to novice users, while providing access to advanced parameters for experts.

Download a free trail version here => http://GenEx.gene-quantification.info

GenEx PDF user guides:
* GenEx user guide 
* GenEx user guide - Exiqon Wizard 
* GenEx user guide - Roche Wizard


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Best regards,
Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

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