deltaXpress (ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data

BMC Bioinformatics

Software

Tatiane Katsue Furuya¹  Alexis Germán Murillo Carrasco¹  Roger Chammas¹  Miyuki Uno¹  Tharcisio Citrangulo Tortelli¹ 

[1] Center for Translational Research in Oncology (LIM24), Instituto Do Cancer Do Estado de Sao Paulo (ICESP), Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), CEP 01246-000, São Paulo, SP, Brazil;Comprehensive Center for Precision Oncology, Universidade de Sao Paulo, São Paulo, Brazil;

关键词: Gene expression;    qPCR;    Shiny;    Gene correlation;    Single-cell analysis;   

DOI  :  10.1186/s12859-023-05541-4

 received in 2023-03-16, accepted in 2023-10-20,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundHigh-throughput experiments provide deep insight into the molecular biology of different species, but more tools need to be developed to handle this type of data. At the transcriptomics level, quantitative Polymerase Chain Reaction technology (qPCR) can be affordably adapted to produce high-throughput results through a single-cell approach. In addition to comparative expression profiles between groups, single-cell approaches allow us to evaluate and propose new dependency relationships among markers. However, this alternative has not been explored before for large-scale qPCR-based experiments.ResultsHerein, we present deltaXpress (ΔXpress), a web app for analyzing data from single-cell qPCR experiments using a combination of HTML and R programming languages in a friendly environment. This application uses cycle threshold (Ct) values and categorical information for each sample as input, allowing the best pair of housekeeping genes to be chosen to normalize the expression of target genes. ΔXpress emulates a bulk analysis by observing differentially expressed genes, but in addition, it allows the discovery of pairwise genes differentially correlated when comparing two experimental conditions. Researchers can download normalized data or use subsequent modules to map differentially correlated genes, perform conventional comparisons between experimental groups, obtain additional information about their genes (gene glossary), and generate ready-to-publication images (600 dots per inch).ConclusionsΔXpress web app is freely available to non-commercial users at https://alexismurillo.shinyapps.io/dXpress/ and can be used for different experiments in all technologies involving qPCR with at least one housekeeping region.

【 授权许可】

CC BY   
© The Author(s) 2023

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