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GenEx
5 downloads (ZIP
and RAR versions) =>
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Compare
GenEx versions
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GenEx Prices
& Upgrading prices for
GenEx 4 to 5 |
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Press review:
GenEx 5.0.1 A Powerful Tool For QPCR Data
Analysis
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.
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 version 5.0.1. of GenEx a 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.
Order here => http://www.multid.se
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GenEx 5.0.1 - Release notes
The first release of
GenEx 5 includes not only bug fixes but also completely new analyses
and new features.
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New analyses
- The optimum number of subject, sample,
RT, and qPCR
replicates can be estimated with the Experimental Design Optimization.
The calculations are based on data from either a pilot study or
estimated variance contributions for each step. The variance for the
design is minimized while keeping under the given budget.
- Analysis of variance for one and two
factors (One-way
ANOVA, Two-way ANOVA) has been implemented to estimate significant
differences between more than two groups. Both include the post hoc
tests Tukey-Kramer procedure, Bonferroni's test, and Dunnett's test.
- Nested ANOVA is used to indicate
significant differences
of between more than two groups in a nested experimental design, but
can also be used to investigate the variance contribution for each
level in the design.
- Support vector machine (SVM) is a new
method found under
the Networks analysis tab in the Enterprise package. It is a
classifying method that, based on already classified samples, builds a
model that is can be used to classify unknown samples.
- Partial least square (PLS) is a
calibrating method that is
found under the Regression analysis tab in the Enterprise package.
Based on known samples, it builds a model that calibrates unknown
samples.
New
features
- Artificial
neural network (ANN) has a new simple interface, but still
offers the
same options under advanced settings.
- The entire
help file have been updated with new texts and pictures.
- Analysis
of variance
(ANOVA) is a group of statistical analyses that, among other
things,
are used to determine whether there is a significant difference of
means between several groups. GenEx 5 offers tests to conclude e.g. if
the expression profiles differ between cancer subtypes (One-way ANOVA),
and e.g. if several treatments affect a set of age groups differently
(Two-way ANOVA). The analysis is done with a simple click of a button!
Most
qPCR experiments have a nested design with technical replicates in each
step, where each step introduces more variance (noise) to the data. The
variance contribution from each step can be analyzed and used to
optimize the experimental design in future experiments. The GenEx
Experimental Design Optimization minimizes the total variation for the
experimental design while keeping the total cost under a given budget.
The Nested ANOVA analysis lets you investigate the variance
contributions, and e.g. see how it changes if you normalize the data
with reference genes.
Variance contributions
for each step in a nested experimental design, absolute values.
Variance contributions for each step in a nested experimental design,
percent of total variance.
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Learn more
For further information of the analyses in
GenEx, see the online manual of the program or contact us.
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Company
MultiD
Analyses AB was the first company with focus on multidimensional data
analyses. It was founded in 2001 by leading scientists and software
engineers from Swedish top universities who discovered that
3-dimensional data may under certain circumstances be decomposed into
contributions from component specific contributions without making
non-trivial assumptions. This opens totally new possibilities to
analyze test samples and study chemical equilibrium, and it was
considered one of the most important discoveries in analytical
chemistry during the 1990-ies.
Our goal is to develop and sell software for analyses of
multidimensional data. Our world unique product, DATAN, based on
proprietary technology, is the most advanced software to analyze
spectroscopic data. Our second unique product, GenEx, is the most
advanced software available to analyze real-time PCR gene expression
data.
Our main competences are in the areas of spectroscopy, fluorescence
detection, data and numerical analysis, chemometry, computing, software
engineering, and real-time PCR.
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GenEx Packages
GenEx comes in three different packages to
fulfill different customer needs: GenEx Standard,
which has all features for basic analyses, GenEx
Professional
which also includes classification methods, and GenEx
Enterprise,
which has all functionalities including advanced expression profiling
analyses. The features available in the three packages are indicated in
the analysis list.
GenEx Standard
GenEx
Standard makes pre-processing of data easy! There are options to
calibrate samples with interpolate calibrators, a number of ways of
handling missing data, and you can correct for primer-dimers and PCR
efficiencies. Samples can also be normalized against reference genes or
reference samples, the sample amounts, or a spike. If technical
replicates have been made, they are easily normalized as well.
GenEx
Standard is often sufficient when only one gene is studied at a time.
It can be used within for example biochemistry or infection
diagnostics. The package includes even more, as can be seen in the analysis list.
The data editor in GenEx
lets you arrange, sort and pre-process the data.
There
are statistical analyses to determine differences between two or more
groups. This includes Student's t-test for paired and unpaired studies,
corresponding non-parametric test, and an ANOVA test for one factor.
You can also cluster your genes or samples in a dendrogram to see for
example which samples show similar expression profiles. There are
several options of letting you visualize the data in a plot including
scatter plots, line plots, a bar plot, as well as a box and whiskers
plot. The plots can be used to efficiently compare expression profiles
of different samples or genes.
Immunoglobulin light chain λ
plotted against κ, where green represents healthy individuals and red
lymphoma positive individuals.
A 3D line plot showing how the
target genes' expressions in yeast changes over time after glucose has
be added to the growth medium.
GenEx Professional
GenEx
Professional includes all analyses in the Standard package and much
more. There are advanced multidimensional analyses such as principal
component analysis (PCA) and self-organized maps (SOM) that lets you
use the expression of several genes to cluster or classify samples.
There are also more advanced statistical tests to determine difference
of means, such as two-way ANOVA which is used when the effect that two
separate factors has on the gene expression. It can be used to
investigate if for instance the studied treatments influence the gene
expression in a set of age groups differently.
This
package is recommended when you are analyzing more than one gene in for
example an exploratory study. This is often done within the medical
field of research. Information of all analysis is included in the analysis list.
The same data shown in
the 3D line plot above is here classified in a SOM. Genes associated
with glycogenesis are shown in red, glycolysis genes in blue and
reference genes in green.
The
package also includes several calibration analyses, such as a standard
curve, reverse calibration to calibrate unknown samples to a standard
curve, and a function to determine the limit of detection (LOD) for
your assay.
A standard curve has
been fitted to measured data (blue line) and is shown with a confidence
interval (red lines). The red dots represent unknown samples.
GenEx Enterprise
Our
most advanced package is the GenEx Enterprise that includes all of the
available analyses. The powerful multidimensional methods artificial
neural networks (ANN) and support vector machines (SVM) let you build a
model of your data that can be used to classify unknown samples in for
example diagnostics. The models are easily shared with other GenEx
users. P-curve is a form of principal component analysis (PCA) that
also lets you classify unknown samples.
GenEx
is excellent tool for predictive studies, when the end product is a
model that can classify or calibrate unknown samples. Typical
applications include diagnostics of complex diseases, and typical users
are pharmaceutical companies. See the analysis list for complete overview of the included analyses.
Two genes have
been used to classify unknown samples with SVM, where red indicates
breast cancer and green indicates no breast cancer.
Several genes
have been used to classify samples from breast cancer patients and
healthy patients with p-curves.
One
of the new features in GenEx 5 is the experimental plan optimization.
It can take data from a previous trial with replicates on each level
(subject, sample, RT, qPCR), estimate the noise that is added at each
level, and suggest an optimal experimental plan for future trials with
minimum total variance under the given budget.
The optimum number of
replicates at each level is presented together with the estimated total
variance and total cost.
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Company
MultiD
Analyses AB was the first company with focus on multidimensional data
analyses. It was founded in 2001 by leading scientists and software
engineers from Swedish top universities who discovered that
3-dimensional data may under certain circumstances be decomposed into
contributions from component specific contributions without making
non-trivial assumptions. This opens totally new possibilities to
analyze test samples and study chemical equilibrium, and it was
considered one of the most important discoveries in analytical
chemistry during the 1990-ies.
Our goal is to develop and sell software for analyses of
multidimensional data. Our world unique product, DATAN, based on
proprietary technology, is the most advanced software to analyze
spectroscopic data. Our second unique product, GenEx, is the most
advanced software available to analyze real-time PCR gene expression
data.
Our main competences are in the areas of spectroscopy, fluorescence
detection, data and numerical analysis, chemometry, computing, software
engineering, and real-time PCR.
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Purchasing GenEx
GenEx can be purchased directly from the
web order page => http://www.multid.se/order/bioeps.php
or from authorized
MultiD representatives => GenEx@gene-quantification.info
or
Sylvia.Pfaffl@BioEPS.com
Genex prices => download PDF
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