qPCR NEWSLETTER - April 2007

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qPCR NEWSLETTER - April 2007

qPCR NEWSLETTER - April 2007

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Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene Quantification homepage. The focus of this newsletter issue is:

- Cluster analysis in real-time PCR
- Error propagation in PCR
- Update of the qPCR Talk and Webinar page
- Online or invisible!
- Real time open qPCR course from 21th - 25th May 2007 at the TATAA Biocenter Prague
- Real time open qPCR course from 2nd - 6th July 2007 in Freising, Germany


Clustering is often one of the first steps in gene expression analysis. How do clustering algorithms work, which ones should we use and what can we expect from them?

Our ability to gather genome-wide expression data has far outstripped the ability of our puny human brains to process the raw data. We can distill the data down to a more comprehensible level by subdividing the genes into a smaller number of categories and then analyzing those. This is where clustering comes in.
The goal of clustering is to subdivide a set of items (in our case, genes) in such a way that similar items fall into the same cluster, whereas dissimilar items fall in different clusters. This brings up two questions: first, how do we decide what is similar; and second, how do we use this to cluster the items? The fact that these two questions can often be answered independently contributes to the bewildering variety of clustering algorithms.
Gene expression clustering allows an open-ended exploration of the data, without getting lost among the thousands of individual genes. Beyond simple visualization, there are also some important computational applications for gene clusters. For example, Tavazoie et al. used clustering to identify cis-regulatory sequences in the promoters of tightly coexpressed genes. Gene expression clusters also tend to be significantly enriched for specific functional categorieswhich may be used to infer a functional role for unknown genes in the same cluster.
In this primer, I focus specifically on clustering genes that show similar expression patterns across a number of samples, rather than clustering the samples themselves (or both). I hope to leave you with some understanding of clustering in general and three of the more popular algorithms in particular. Where possible, I also attempt to provide some practical guidelines for applying cluster analysis to your own gene expression data sets.


- How does gene expression clustering work?
- Evaluation of gene-expression clustering via mutual information distance measure.
- How to infer gene networks from expression profiles.
- Distribution-insensitive cluster analysis in SAS on real-time PCR gene expression data of steadily expressed genes.
- A new molecular breast cancer subclass defined from a large scale real-time quantitative RT-PCR study.
- Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators.
- An approach for clustering gene expression data with error information.
- Expression profiles and biological function.
- Smoking and cancer-related gene expression in bronchial epithelium and non-small-cell lung cancers.


Error propagation in PCR:


- A general model of error-prone PCR.
- Error propagation in relative real-time reverse transcription polymerase chain reaction quantification models: The balance between accuracy and precision.
- A quantitative model of error accumulation during PCR amplification.
- Real Time PCR: A useful new approach? Statistical Problems?


Power Calculator - NEW links !

This article focuses on how to do meaningful power calculations and sample-size determination for common study designs. There are 3 important guiding principles. First, certain types of retrospective power calculations should be avoided, because they add no new information to an analysis. Second, effect size should be specified on the actual scale of measurement, not on a standardized scale. Third, rarely can a definitive study be done without first doing a pilot study. Some simple examples as well as a complex example are given. Power calculations are illustrated using Java applets developed by the author.



TALKS Update of the qPCR Talk and Webinar page

A lot of interesting TALKs, WEBINARs, SLIDE SHOWs, and PODCASTs from various speakers, companies, qPCR Events, and journals (Nature and Science) are FREE for download. Have a look and you will definitely something interesting for your scientific work !




CITATION Online or invisible!

Articles freely available online are more highly cited. For greater impact and faster scientific progress, authors and publishers should aim to make research easy to access.



Real time open qPCR course from 21th - 25th May 2007 at the TATAA Biocenter Prague



TATAA Biocenter Germany - qPCR Application workshops


At the TATAA Biocenter Germany we offer qPCR application workshops, the 3-day Core Module and a 2-day Biostatistics Module. qPCR courses are held in regularly in Gteborg, Sweden in English and in Freising-Weihenstephan, Germany in German and English. Depending on the occasion the workshop language and the different prices may apply. Further customized workshops and specialized trainings will be held as well across Europe and world-wide. TATAA Biocenter Germany courses are held in cooperation with the Institute of Physiology, located at the Technical University of Munich, in Freising-Weihenstephan, near Munich, very close to the Munich Airport (MUC). For more information and to register for the qpCR application workshops, please see our web page: http://tataa.gene-quantification.info/

Course Occasions 2007: Please register here: http://www.tataa.com/

- 2nd - 6th July (in English) 3-day Core module and 2-day BioStatistics Module


Forward Please send the qPCR NEWS to further scientists and friends who are interested in qPCR and in our Academic & Industrial Information Platform for qPCR.

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

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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 Michael W. Pfaffl and powered by BioScience Events. Copyright 2005 - 2007 All rights reserved. Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. Disclaimer & Copyrights are displayed on the homepage www.gene-quantification.com To subscribe or change your e-mail address in qPCR NEWS, and if you would like to receive future issues FREE of charge, please send an e-mail with the subject SUBSCRIBE