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ICESP/FMUSP researcher launches new version of app developed to map differentially correlated genes

Visual abstract presents a summary of the app’s features. Img: Reproduction

Dr. Alexis Germán Murillo Carrasco, researcher at the Translational Oncology Center (CTO) of the Instituto do Câncer do Estado de São Paulo (ICESP) and the Faculdade de Medicina da Universidade de São Paulo (FMUSP), has launched a new version of deltaXpress (ΔXpress), a software application for mapping differentially correlated genes using single-cell qPCR (quantitative Polymerase Chain Reaction) data.

The deltaXpress application, initially launched in 2023, can be used to propose biomarkers from experiments using single-cell or multi-sample qPCR data. In addition to the application, a publication has been prepared for the journal BMC Bioinformatics, detailing the functionality of the software.

According to the publication, along with conventional strategies for comparing expression levels between groups of genes (Differential Expression Analysis), the analysis of co-dependent genes (Differential Correlation Analysis) can be helpful in understanding various mechanisms of gene regulation.

The application features seven modules, which users can navigate through the top menu bar. Usage begins in the first module, Input, where the user should upload a file with amplification value (Cycle threshold, Ct) information in one of the accepted formats (.xls, .xlsx, .txt, or .csv). The information should be arranged as follows: a first column with sample names, a second column with a group classification, and the following columns with Ct values for all genes analyzed (including normalization genes).

Once the file is uploaded, simply press the “Start!” button to normalize the data, and the other six modules will activate, displaying the analyzed information. These modules include: Data Normalization, Expression Analysis, Volcano Plots, Correlation Analysis, Scatter Plots, and Glossary. The application also produces publication-ready images for scientific presentations.

According to Dr. Alexis Carrasco: “This new version of the application allows for a streamlined data processing experience for gene expression experiments, offering simplicity and practicality while maintaining statistical accuracy, transparency, and reproducibility in analyses. Thanks to the testing phase conducted by researchers and residents in our lab, we have enhanced the application with new features. Now, users can personalize result displays by choosing colors for each experimental group, making the experience more dynamic.”

Development also included contributions from other ICESP/FMUSP researchers: Dr. Tatiane Katsue Furuya, Dr. Miyuki Uno, Dr. Tharcísio Citrangulo Tortelli Jr., and Prof. Dr. Roger Chammas.

The deltaXpress tool is available online, free of charge, and is intended for non-commercial use.

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