Analyzing integrated network of methylation and gene expression profiles in lung squamous cell carcinoma

被引:3
作者
Heryanto, Yusri Dwi [1 ]
Katayama, Kotoe [2 ]
Imoto, Seiya [1 ,2 ]
机构
[1] Univ Tokyo, Human Genome Ctr, Inst Med Sci, Div Hlth Med Intelligence, Tokyo, Japan
[2] Univ Tokyo, Human Genome Ctr, Inst Med Sci, Lab Sequence Anal, Tokyo, Japan
关键词
PROTEIN; CANCER; FOXP1; LISTS;
D O I
10.1038/s41598-022-20232-5
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Gene expression, DNA methylation, and their organizational relationships are commonly altered in lung squamous cell carcinoma (LUSC). To elucidate these complex interactions, we reconstructed a differentially expressed gene network and a differentially methylated cytosine (DMC) network by partial information decomposition and an inverse correlation algorithm, respectively. Then, we performed graph union to integrate the networks. Community detection and enrichment analysis of the integrated network revealed close interactions between the cell cycle, keratinization, immune system, and xenobiotic metabolism gene sets in LUSC. DMC analysis showed that hypomethylation targeted the gene sets responsible for cell cycle, keratinization, and NRF2 pathways. On the other hand, hypermethylated genes affected circulatory system development, the immune system, extracellular matrix organization, and cilium organization. By centrality measurement, we identified NCAPG2, PSMG3, and FADD as hub genes that were highly connected to other nodes and might play important roles in LUSC gene dysregulation. We also found that the genes with high betweenness centrality are more likely to affect patients' survival than those with low betweenness centrality. These results showed that the integrated network analysis enabled us to obtain a global view of the interactions and regulations in LUSC.
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页数:13
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