Functional enrichment analysis of MIB1 promoter and interacting genes in zebrafish
10.3969/j.issn.1673-4130.2023.24.004
- VernacularTitle:斑马鱼MIB1启动子及互作基因的功能富集分析
- Author:
Fan WANG
1
;
Shiming XU
;
Wen YAN
;
Tongnan GU
;
Hongjuan WANG
Author Information
1. 首都医科大学燕京医学院生物化学与分子生物学教研室,北京 101300
- Keywords:
bioinformatics;
E3 ubiquitin protein ligase 1;
promoter;
transcription factor binding site;
interacting genes
- From:
International Journal of Laboratory Medicine
2023;44(24):2963-2969
- CountryChina
- Language:Chinese
-
Abstract:
Objective To analyze the transcription factor binding sites(TFBS)in the promoter region of E3 ubiquitin protein ligase 1(MIB1)gene in zebrafish,the types of MIB1 interacting genes and proteins and their roles in signaling pathways,and to investigate the regulatory mode and potential function of MIB1 gene.Methods Non-coding RNA(ncRNA)was predicted by National Genomics Data Center(NGDC).Alggen and AnimalTFDB online software were used to predict the TFBS types of MIB1 gene.GeneMANIA and STRING were used to analyze the interacting genes and proteins of MIB1.The related data were obtained through DA-VID website,and gene ontology(GO)visual analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)metabolic pathway analysis were performed.Results ncRNA could be transcribed from the promot-er region and 5'untranslated region of MIB1 gene.A total of 121 TFBS were obtained by prediction.P53 tran-scription factor could bind to the promoter region of MIB1 gene and interact with MIB1 protein.A total of 6 co-expressed genes of MIB1 were predicted online,and 20 interacting genes were screened.GO visual analysis showed that MIB1 and its interaction genes had functions in regulating the growth and differentiation of cells,tissues and organs and regulating the NOTCH signaling pathway in the biological process,and were mainly enriched in the cytoplasmic perinuclear region,cell membrane,postsynaptic dense area and so on.It had molec-ular functions such as binding NOTCH proteins and PDZ domain proteins.KEGG metabolic pathway analysis showed that MIB1 and its interacting genes were involved in 4 metabolic pathways.Conclusion MIB1 con-tains a variety of TFBS,and affects a variety of biological processes such as cell carcinogenesis and immune regulation by interacting with specific transcription factors.MIB1 may also play an important role in cell growth regulation,hematopoietic stem cell differentiation,embryonic development and neuronal information transmission through the mediation of its interacting genes and proteins.
