GenEx

GenEx is a specialized software created for the preprocessing, analysis, and visualization of gene expression data derived from real-time quantitative PCR (qPCR) and digital PCR (dPCR) experiments. It is utilized in academic research, biotechnology labs, and regulated settings due to its modular design and analytical features.

GenEx
Developer(s)	MultiD Analyses AB
Stable release	GenEx 8.0 & GeneEx GxP / 2025
Operating system	Windows
Type	Gene expression analysis
License	Proprietary
Website	multid.se

The software is designed to simplify the intricate task of interpreting PCR data, providing tools for normalization, statistical evaluation, and graphical depiction of gene expression outcomes. Its architecture accommodates a broad spectrum of experimental designs and adheres to MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) standards.

History

GenEx was created by MultiD Analyses AB, a Swedish firm established in 2001 by scientists and software engineers from universities in Sweden.^[1]

The early iterations of GenEx were crafted to meet the increasing demand for reliable and user-friendly tools for analyzing real-time quantitative PCR (qPCR) data. As PCR technologies advanced in gene expression research, GenEx became a premier solution for data preprocessing, normalization, and statistical evaluation.^[2]

In 2019, the launch of GenEx 7.0 represented a major advancement in the software’s evolution. This version achieved full compliance with MIQE guidelines and CLSI standards, which are essential for maintaining data quality and reproducibility in regulated settings such as clinical diagnostics and pharmaceutical research. GenEx 7.0 also included features to encompass multivariate techniques like principal component analysis (PCA), hierarchical clustering, and self-organizing maps (SOM), along with machine learning capabilities such as artificial neural networks (ANN) and support vector machines (SVM) for sample classification and biomarker identification.^[3] In the early 2025, GenEx 8 and GenEx Gxp versions were released.^[4]

Editions

• GenEx 8.0: is the latest GenEx software version for gene expression data analysis, supporting research and applications in biology, pharmaceuticals, and diagnostics.

• GenEx GxP: is a software designed for bioanalytical and diagnostic laboratories, supporting qPCR and dPCR data analysis in regulated environments.

Features

Data Preprocessing

GenEx software facilitates the import and conversion of a range of file formats from leading qPCR and dPCR instrument manufacturers, such as Applied Bio systems, Bio-Rad, and Roche. It features quality control tools like outlier detection, amplification efficiency assessment, and sample integrity evaluation. Also, the software provides various normalization methods, including reference gene normalization, global mean normalization, and normalization using external controls.^[5]

Analysis Tools

GenEx offers both relative and absolute quantification techniques. Relative quantification utilizes comparative methods like the ΔΔCt approach to assess changes in gene expression. Absolute quantification is accomplished through standard curve-based methods, allowing for accurate measurement of target copy numbers. The software also features efficiency correction capabilities to address variations in amplification efficiency across different assays. For multivariate statistical analysis, GenEx includes principal component analysis (PCA), hierarchical clustering, and self-organizing maps (SOM), which aid in pattern recognition and sample classification.^[6][7]

Visualization

The software produces publication-quality graphical representations, such as bar charts, scatter plots, heatmaps, and amplification curves. Interactive dashboards enable users to dynamically explore data, with customizable views and filtering options to improve interpretability.^[8]

Applications

GenEx is employed in various areas of the life sciences. In molecular biology, it is used to analyze gene expression profiles under diverse experimental conditions. In clinical research, the software assists in the discovery and validation of biomarkers for disease diagnostics and prognostics. Agricultural biotechnology applications encompass gene expression studies in genetically modified organisms and research on crop enhancement. In pharmaceutical development, GenEx facilitates investigations into drug efficacy and toxicity related to gene regulation.^[9]

GenEx supports a wide variety of qPCR and dPCR platforms, including Thermo Fisher / ABI (QuantStudio, ViiA7, StepOne), Bio‑Rad CFX, Roche LC, Fluidigm Biomark, Illumina ECO, Agilent AriaMX/MX3000, Rotorgene, AnalytikJena, WaferGene, and 3D‑Gene microRNA chips.^[10]

See Also

MIQE