Identification of Critical Modules and Biomarkers of Ulcerative Colitis by Using WGCNA.
bioinformatics analysis
biomarkers
ceRNA regulatory network
hub genes
ulcerative colitis
Journal
Journal of inflammation research
ISSN: 1178-7031
Titre abrégé: J Inflamm Res
Pays: New Zealand
ID NLM: 101512684
Informations de publication
Date de publication:
2023
2023
Historique:
received:
10
01
2023
accepted:
28
03
2023
medline:
24
4
2023
pubmed:
24
4
2023
entrez:
24
04
2023
Statut:
epublish
Résumé
Ulcerative colitis (UC) is a chronic inflammatory disease of the colon and rectum that has no exact cause and is characterized by relapsing and remitting episodes. We aimed to find biomarkers of UC and its causes. We got GSE73661 from the GEO database and used WGCNA to find DEGs that were expressed in the same way in both normal and UC samples. To identify the co-expression modules, we used Weighted Gene Co-Expression Network Analysis. Next, we selected genes that were both DEGs and parts of main modules. Later, three datasets were used to find the hub genes, and qRT-PCR was utilized to confirm the in-silico findings. Additionally, we analyzed the connection between the hub genes and the filtration of immune cells in UC. Using the databases, we made predictions about the miRNAs and lncRNAs that regulate the hub genes and predicted possible therapeutic drugs. We found 822 DEGs and three main modules related to immunity, endoplasmic reticulum, and metabolism. Using another three datasets and human samples to confirm the mRNA expression of these genes in UC patients, XBP1 and PLPP1 were selected as hub genes, and had excellent diagnostic potential. According to the findings of the immune infiltration, patients with UC exhibited a larger proportion of immune cells. And hub genes, particularly XBP1, were closely linked to a number of immune cell infiltrations. Based on the databases and hub genes, a lncRNA-miRNA-mRNA network, including two miRNAs (miR-214-3p and miR-93-5p), two hub genes, and 124 lncRNAs, and potential therapeutic medicine were identified. We found two new genes, XBP1 and PLPP1, that are involved in UC and can help diagnose and measure the disease. XBP1 also relates to clinical scores and immune cells. We suggested a gene network and possible drugs based on them.
Sections du résumé
Background
UNASSIGNED
Ulcerative colitis (UC) is a chronic inflammatory disease of the colon and rectum that has no exact cause and is characterized by relapsing and remitting episodes. We aimed to find biomarkers of UC and its causes.
Methods
UNASSIGNED
We got GSE73661 from the GEO database and used WGCNA to find DEGs that were expressed in the same way in both normal and UC samples. To identify the co-expression modules, we used Weighted Gene Co-Expression Network Analysis. Next, we selected genes that were both DEGs and parts of main modules. Later, three datasets were used to find the hub genes, and qRT-PCR was utilized to confirm the in-silico findings. Additionally, we analyzed the connection between the hub genes and the filtration of immune cells in UC. Using the databases, we made predictions about the miRNAs and lncRNAs that regulate the hub genes and predicted possible therapeutic drugs.
Results
UNASSIGNED
We found 822 DEGs and three main modules related to immunity, endoplasmic reticulum, and metabolism. Using another three datasets and human samples to confirm the mRNA expression of these genes in UC patients, XBP1 and PLPP1 were selected as hub genes, and had excellent diagnostic potential. According to the findings of the immune infiltration, patients with UC exhibited a larger proportion of immune cells. And hub genes, particularly XBP1, were closely linked to a number of immune cell infiltrations. Based on the databases and hub genes, a lncRNA-miRNA-mRNA network, including two miRNAs (miR-214-3p and miR-93-5p), two hub genes, and 124 lncRNAs, and potential therapeutic medicine were identified.
Conclusion
UNASSIGNED
We found two new genes, XBP1 and PLPP1, that are involved in UC and can help diagnose and measure the disease. XBP1 also relates to clinical scores and immune cells. We suggested a gene network and possible drugs based on them.
Identifiants
pubmed: 37092131
doi: 10.2147/JIR.S402715
pii: 402715
pmc: PMC10120594
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1611-1628Informations de copyright
© 2023 Yuan et al.
Déclaration de conflit d'intérêts
The authors declare that they have no competing interests.
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