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Tracking significant modules and key genes for esophageal squamous cell carcinoma based on differential modules


1 Department of Chest Surgery, The 309th Hospital, PLA, Beijing 100091, China
2 Department of Chest Surgery, General Hospital, PLA, Beijing 100853, China
3 Department of General Surgery, Peking University International Hospital, Beijing 100026, China

Correspondence Address:
Meng-Li Zheng,
Department of Chest Surgery, The 309th Hospital, PLA, No. 17, Heishanhujia Road, Haidian District, Beijing 100091
China
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Source of Support: None, Conflict of Interest: None

Background: The exact molecular mechanism of esophageal squamous cell carcinoma (ESCC) is still unknown, and the prognosis of ESCC has not been significantly improved. Objective: To understand the molecular mechanism of ESCC, differential modules (DMs) and key genes were identified through conducting analysis on the differential co-expression network (DCN) based on the gene expression profiles of ESCC and protein-protein interaction (PPI) data. Materials and Methods: First, gene expression profiles of ESCC and PPI data recruiting and preprocessing were conducted; then, a DCN was constructed based on the gene co-expression and gene differential expression in ESCC; in the following, candidate DMs were mined from DCN through a systemic module searching strategy, and significance analysis was performed on candidate DMs to identify DMs; moreover, significant genes contained in the DMs were analyzed to identify the underlying biomarkers for ESCC. Finally, pathway enrichment analysis was conducted to disclose the function of these DMs. Results: A total of 10,975 genes were obtained after comprehensively preprocessing on the gene expression profiles and PPI data. Then, a DCN with 915 nodes (1164 interactions) was built, and 45 seed genes were identified. In the following, four DMs that separately enriched in phenylalanine metabolism, nicotine addiction, phenylalanine metabolism, and B-cell receptor signaling pathway were identified, where module 1 and module 3 were all enriched in phenylalanine metabolism pathway. Furthermore, the most significant seed gene myeloperoxidase (MPO) was contained in all of the DMs. Conclusions: In this study, we successfully identified 4 DMs, three significant pathways, and a key gene MPO in ESCC, which might play key roles during the occurrence and development of ESCC and could be chosen as good indicators and therapeutic schedule for ESCC.


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    -  Zheng ML
    -  Zhou NK
    -  Luo CH
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