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GenEx offers
advanced methods to
analyze real-time
qPCR data with
simple mouse clicks
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 real-time PCR
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 7.0
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,
Hierarchical Cluster
Analysis (HCA), Heatmap,
Principal Component Analysis
PCA), 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 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.
Please see
our Online
Tutorials
TATAA
and MultiD launch GenEx
7.0 – the software
compliant with MIQE
and CLSI
guidelines
launched May
2019
TATAA
Biocenter, Europe´s
leading provider of genomic
services using quantitative
real-time PCR (qPCR), and MultiD
Analyses, Europe’s
prime software developer for
the analysis of multivariate
data, release GenEx version
6 for accurate analysis of
qPCR data compliant with
current MIQE
guidelines and
Clinical
Laboratory
Standards Institute
(CLSI) guidelines (description
below).
The new analyses in
GenEx 7.0 include:
Estimating PCR efficiency,
testing for outliers,
testing linear model,
estimating dynamic range,
estimating random error,
estimating limit of
detection, estimating limit
of quantification,
estimating concentrations of
unknowns, evaluation of
precision, and verification
of precision. For all
estimates confidence
intervals are
calculated. ...
and much more ...
download 14 days free
trial version!
Additional new features
include: transcript
distribution for single cell
analysis, Survival Analysis,
Receiver Operator
Characteristics (ROC),
Wizard for ProSeek protein
analysis, and reader for
3DGene microRNA analysis.
“I have been
using GenEx for all my
qPCR analyses for the
past 5 years. With GenEx
I can be sure that my
data normalization and
analyses will be MIQE
compliant. Whether I’m
analyzing qPCR arrays,
data with a standard
curve or determining a
relative difference, it
takes little time to
import the files I need
and obtain my final data
set”
says Greg Shipley,
President of Shipley
Consulting, LLC.
“We have been
using GenEx for many
years at Technical
University of Munich.
With every new released
version we are impressed
by the many clever
functionalities
introduced for RT-qPCR
analysis, especially the
data normalisation and
visualisation tools like
PCA or HCA”,
“The new CLSI
compliant analyses are
most interesting to us
and a natural extension
of the MIQE guidelines”
says
Michael W. Pfaffl.
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Join
all GenEx talks held at
our qPCR Events - eConferences.de
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Genex data import
from various qPCR cycler
platforms:
Most
instruments
are able to export qPCR
data as text export files
(*.txt). GenEx is designed
to easily import qPCR data
from these export files in
order to remove the need
of manually rearranging
data in Excel.
List
of supported qPCR
instruments by GenEx™
- Thermo Fisher/ABI
EDS files
- QuantStudio 12K
Flex (384 and 96 Wells)
- QuantStudio
OpenArray
(ExpressionSuite)
- ViiA7 (384 and 96
Wells)
- ABI 7900 (384 and
96 Wells)
- ABI 7500 (96
Wells)
- ABI 7300 (96
Wells)
- ABI StepOne
- ABI RQ Manager
for SDS 2.3 or SDS
2.4 (384 and 96
Wells)
- BioRad CFX
Manager V2 and V3 (384
and 96 Wells)
- Roche LC480 (384
and 96 Wells)
- Roche LC96
- Illumina ECO
- Biomark (Fluidigm
96 X 96 48 X
48 192 X 24)
HeatMap
- Biomark (Fluidigm
96 X 96 48 X
48 192 X 24) Table
- Agilent
MX3000/3005
- Agilent AriaMX
- 3D-Gene (TORAY
miRNA Chips)
- AnalytikJena
- AnalytikJena
Export Tool
- Rotorgene
- Thermo PikoReal
- Douglas
Scientific IntelliQube
- WaferGene export
files
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GenEx 7.0
-- Release notes
The first
release of GenEx 7.0 includes not
only bug fixes but also completely
new analyses and new features.
We are proud to release GenEx 7.0
which is the most power qPCR
analysis software so far!
Among
the new features you find
comprehensive CLSI compliant
analysis, which satisfies the
requirements of regulatory
bodies, including:
- Estimating PCR efficiency
from standard curve, including
confidence interval
- Testing for outliers in a
qPCR standard curve
- Testing for linear model
in a qPCR standard curve
- Testing for dynamic range
in a qPCR standard curve
- Estimating random error
of a qPCR standard curve
- Estimating limit of
detection including confidence
interval of a qPCR assay/test
- Estimating limit of
quantification of a qPCR
assay/test
- Estimating concentrations
including confidence intervals
of unknowns based on qPCR
standard curve
- Evaluation of Precision
of a qPCR assay/test
- Verification of precision
of a qPCR assay/test
Other New Analysis
Features include:
- Histogram plot for single
cell analysis
- Repeated Measures ANOVA
- Survival Analysis
- Receiver Operator
Characteristics (ROC)
- Wizard for ProSeek
protein analysis by means of PEA
(Olink)
News in GenEx update
7.0
- In Import Wizard
- Reader for Fluidigm Biomark
Table format.
- Reader for Thermo Fisher
/ABI EDS files
- Reader for Douglas
Scientific InteliQube
- Reader for BioRad CFX
manager V3
- Option for removing or
keeping "999" values in
Biomark reader
- In Data Editor
- Adding function "Show
frequency of missing data
groupwise"
- Adding Submenu "Sort by
classification column"
- Warning generates if
correction for Valid Prime is
larger than 1 cycle
- In DataManager
- Adding ability to create
classification columns based
on the defined groups
... and much more!
New
licensing options:
- GenEx Licensing
Time limited licenses are
available for 6, 12 and 24
months. Updates for the license
version are for free.
- Desktop license: License
locked to one computer.
Network concurrent Licensing:
Minimum of 5 licenses setup in a
network allowing GenEx to be
activated on any computer with
access to the network. Only
available with perpetual
license.
- System Requirements
Any modern computer running
Microsoft Windows XP or later, 4
GB of RAM (8 GB or more
recommended), 80 MB of available
hard-disk space, display with
resolution 1024 by 768 pixels or
higher and scale 96 DPI. Mac
users will need "Parallel" or
"VM-Ware" virtual environment to
run Windows.
... just download
your 14 days trial version!
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Heatmap |
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Volcano plot |
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limit
of detection (LOD)
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Limit of quantification
(LOQ)
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dynamic PCA |
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HCA
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GenEx
Packages
GenEx comes in three
different packages to
fulfill different customer needs:
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.
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| The data editor in
GenEx lets you arrange, sort and
pre-process the data. |
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Immunoglobulin
light chain λ plotted against κ,
where green represents healthy
individuals and red lymphoma
positive individuals. |
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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. |
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| A 3D line plot
showing how the target genes'
expressions in yeast changes over
time after glucose has be added to
the growth medium. |
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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 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.
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| 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. |
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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. |
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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
anlysis for complete overview of
the included analyses.
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| Two genes
have been used to classify unknown
samples with SVM, where red
indicates breast cancer and green
indicates no breast cancer. |
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Several genes have
been used to classify samples from
breast cancer patients and healthy
patients with p-curves. |
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| One
of
the new features in GenEx 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. |
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| The optimum number
of replicates at each level is
presented together with the
estimated total variance and total
cost. |
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Clinical
Laboratory
Standards Institute (CLSI)
The EP5
module in Genex implements
the statistical analyses required by
the guidelines in the CLSI
document EP05-A2 Evaluation of
Precision Performance
ofQuantitative Measurement
Methods; Approved Guidelines -
Second Edition.
The purpose of EP05 is to evaluate
the precision of clinical laboratory
measurementmethods. The EP05
guidelines are intended both for
developers of such methods and for
users of methods who want to verify
the validity of given precision
claims, or just measure their own
precision.
CLSI
document EP05-A3
-- Evaluation of
Precision Performance
ofQuantitative Measurement
Methods; Approved
Guidelines (3rd Edition)
The EP15 module in Genex
implements the statistical analyses
required by the guideline in the CLSI
document EP15-A2 User Verification
of Performance for Precision and
Trueness; Approved Guideline -
Second Edition.
The purpose of EP15 is to verify the
performance of a method whose
performance has previously been
established by more extensive
protocols. EP15 verifies the
within-runprecision (the
repeatability) and the
within-laboratory precision. EP15
also verifies thetrueness of the
method, by estimating its bias from
a reference value or reference
method. We give below some of the
main features of the EP15 guideline,
for a detailed description see the
EP15-A2 document.
CLSI
document EP15-A3 -- User
Verification of Performance for
Precision and Trueness;
Approved Guideline (3rd Edition)
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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 7.0 -- price
list and supported instruments
GenEx
can be purchased directly
from bioMCC (woldwide
authorized MultiD
representative)
=> GenEx@bioMCC.com
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