Document Type
Article
Publication Date
4-2-2024
Original Citation
Rinchai D,
Brummaier T,
A Marr A,
Habib T,
Toufiq M,
Kino T,
Nosten F,
Al Khodor S,
Terranegra A,
McGready R,
Kabeer B,
Chaussabel D.
A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings. Database (Oxford). 2024;2024:baae021.
Keywords
JGM, Pregnancy, Humans, Female, Transcriptome, Pregnant Women, Software, Gene Expression Profiling, Databases, Genetic
JAX Source
Database (Oxford). 2024;2024:baae021.
ISSN
1758-0463
PMID
38564425
DOI
https://doi.org/10.1093/database/baae021
Abstract
Transcriptome profiling data, generated via RNA sequencing, are commonly deposited in public repositories. However, these data may not be easily accessible or usable by many researchers. To enhance data reuse, we present well-annotated, partially analyzed data via a user-friendly web application. This project involved transcriptome profiling of blood samples from 15 healthy pregnant women in a low-resource setting, taken at 6 consecutive time points beginning from the first trimester. Additional blood transcriptome profiles were retrieved from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) public repository, representing a cohort of healthy pregnant women from a high-resource setting. We analyzed these datasets using the fixed BloodGen3 module repertoire. We deployed a web application, accessible at https://thejacksonlaboratory.shinyapps.io/BloodGen3_Pregnancy/which displays the module-level analysis results from both original and public pregnancy blood transcriptome datasets. Users can create custom fingerprint grid and heatmap representations via various navigation options, useful for reports and manuscript preparation. The web application serves as a standalone resource for exploring blood transcript abundance changes during pregnancy. Alternatively, users can integrate it with similar applications developed for earlier publications to analyze transcript abundance changes of a given BloodGen3 signature across a range of disease cohorts. Database URL: https://thejacksonlaboratory.shinyapps.io/BloodGen3_Pregnancy/.
Comments
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.