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Novel genes associated with folic acid-mediated metabolism in mouse: A bioinformatics study
Jianwen Zhao1, Wen Zou2, Tingxi Hu1
1Shenyang Medical College, Shenyang, Liaoning, China.
Abstract:
Folic acid plays an essential role in the central nervous system and cancer. This study aimed to screen genes related to folic acid metabolism. Datasets (GSE80587, GSE65267 and GSE116299) correlated to folic acid were screened in the Gene Expression Omnibus. Weighed gene co-expression network analysis was performed to identify modules associated with sample traits of folic acid and organs (brain, prostate and kidney). Functional enrichment analysis was performed for the eigengenes in modules that were significantly correlated with sample traits. Accordingly, the hub genes and key nodes in the modules were identified using the protein interaction network. A total of 17,252 genes in three datasets were identified. One module, which included 97 genes that were highly correlated with sample traits (including folic acid treatment [cor = -0.57, P = 3e-04] and kidney [cor = -0.68, p = 4e-06]), was screened out. Hub genes, including tetratricopeptide repeat protein 38 (Ttc38) and miR-185, as well as those (including Sema3A, Insl3, Dll1, Msh4 and Snai1) associated with "neuropilin binding", "regulation of reproductive process" and "vitamin D metabolic process", were identified. Genes, including Ttc38, Sema3A, Insl3, Dll1, Msh4 and Snai1, were the novel factors that may be associated with the development of the kidneys and related to folic acid treatment.
Insights
Folic acid is vital for the brain and cancer. This study identified novel genes, including Ttc38 and Sema3A, associated with kidney development and folic acid treatment.
Area of Science:
- Genomics and Bioinformatics
- Molecular Biology
- Developmental Biology
Background:
- Folic acid is crucial for central nervous system function and cancer development.
- Understanding folic acid metabolism is key to identifying therapeutic targets.
- Gene expression patterns offer insights into biological processes affected by folic acid.
Purpose of the Study:
- To screen genes involved in folic acid metabolism.
- To identify key genes and pathways associated with folic acid in specific organs.
- To uncover novel factors potentially influencing kidney development and folic acid response.
Main Methods:
- Utilized weighted gene co-expression network analysis (WGCNA) on three Gene Expression Omnibus datasets (GSE80587, GSE65267, GSE116299).
- Performed functional enrichment analysis on significant gene modules.
- Identified hub genes and key nodes using protein-protein interaction networks.
Main Results:
- A module of 97 genes showed a strong correlation with folic acid treatment and kidney traits.
- Identified hub genes such as tetratricopeptide repeat protein 38 (Ttc38) and miR-185.
- Discovered novel genes (Sema3A, Insl3, Dll1, Msh4, Snai1) linked to "neuropilin binding", "regulation of reproductive process", and "vitamin D metabolic process".
Conclusions:
- Tetratricopeptide repeat protein 38 (Ttc38), Sema3A, Insl3, Dll1, Msh4, and Snai1 are novel factors potentially involved in kidney development.
- These genes may play a role in the biological response to folic acid treatment.
- This research provides a foundation for further investigation into folic acid's role in renal health and disease.
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