Environmental pathways affecting gene expression (E.PAGE) as an R package to predict gene-environment associations.
Sci Rep
; 12(1): 18710, 2022 11 04.
Article
in En
| MEDLINE
| ID: mdl-36333579
ABSTRACT
The purpose of this study is to manually and semi-automatically curate a database and develop an R package that will act as a comprehensive resource to understand how biological processes are dysregulated due to interactions with environmental factors. The initial database search run on the Gene Expression Omnibus and the Molecular Signature Database retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 237 datasets were selected and 522 gene modules were manually annotated. We then curated a database containing four environmental factors, cigarette smoking, diet, infections and toxic chemicals, along with a total of 25,789 genes that had an association with one or more of gene modules. The database and statistical analysis package was then tested with the differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, COVID-19, cobalt exposure and smoking. On testing, we uncovered statistically enriched biological processes, which revealed pathways associated with environmental factors and the genes. The curated database and enrichment tool are available as R packages at https//github.com/AhmedMehdiLab/E.PATH and https//github.com/AhmedMehdiLab/E.PAGE respectively.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Gene Expression Profiling
/
COVID-19
Type of study:
Prognostic_studies
/
Risk_factors_studies
Limits:
Humans
Language:
En
Journal:
Sci Rep
Year:
2022
Document type:
Article
Affiliation country:
Australia