Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma
Abstract Background The incidence of nasopharyngeal carcinoma (NPC) is rare, but a certain amount of mortality remains in NPC patients. Our study aimed to identify candidate genes as biomarkers for NPC screening, diagnosis, and therapy. Methods We investigated two microarray profile datasets GSE6463...
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| Format: | Article |
| Language: | English |
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BMC
2019-04-01
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| Series: | World Journal of Surgical Oncology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12957-019-1605-9 |
| _version_ | 1818162067115343872 |
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| author | Zhimin Ye Fangzheng Wang Fengqin Yan Lei Wang Bin Li Tongxin Liu Fujun Hu Mingxiang Jiang Weiyang Li Zhenfu Fu |
| author_facet | Zhimin Ye Fangzheng Wang Fengqin Yan Lei Wang Bin Li Tongxin Liu Fujun Hu Mingxiang Jiang Weiyang Li Zhenfu Fu |
| author_sort | Zhimin Ye |
| collection | DOAJ |
| description | Abstract Background The incidence of nasopharyngeal carcinoma (NPC) is rare, but a certain amount of mortality remains in NPC patients. Our study aimed to identify candidate genes as biomarkers for NPC screening, diagnosis, and therapy. Methods We investigated two microarray profile datasets GSE64634 and GSE12452 to screen the potential differentially expressed genes (DEGs) in NPC. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs were also performed. A protein-protein interaction (PPI) network of DEGs was constructed by STRING and visualized by Cytoscape software. The associated transcriptional factor regulatory network of the DEGs was also constructed. Results A total of 152 DEGs were identified from the GSE64634 and GSE12452 datasets, including 10 upregulated and 142 downregulated genes. Gene functional enrichment analysis indicated that these DEGs were enriched in the cilium movement, antimicrobial humoral response, O-glycan processing, mucosal immune response, carbohydrate transmembrane transporter activity, hormone biosynthetic process, neurotransmitter biosynthetic process, and drug metabolism-cytochrome P450 pathway. Five hub genes (DNALI1, RSPH4A, RSPH9, DNAI2, and ALDH3A1) and one significant module (score = 5.6) were obtained from the PPI network. Key transcriptional factors, such as SPI1, SIN3B, and GATA2, were identified with close interactions with these five hub DEGs from the gene-transcriptional factor network. Conclusions With the integrated bioinformatic analysis, numerous DEGs related to NPC were screened, and the hub DEGs we identified may be potential biomarkers for NPC. |
| first_indexed | 2024-12-11T16:27:46Z |
| format | Article |
| id | doaj.art-37f99126ceb24dc9928eee90fbb96db4 |
| institution | Directory Open Access Journal |
| issn | 1477-7819 |
| language | English |
| last_indexed | 2024-12-11T16:27:46Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | World Journal of Surgical Oncology |
| spelling | doaj.art-37f99126ceb24dc9928eee90fbb96db42022-12-22T00:58:41ZengBMCWorld Journal of Surgical Oncology1477-78192019-04-0117111010.1186/s12957-019-1605-9Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinomaZhimin Ye0Fangzheng Wang1Fengqin Yan2Lei Wang3Bin Li4Tongxin Liu5Fujun Hu6Mingxiang Jiang7Weiyang Li8Zhenfu Fu9Department of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalDepartment of Radiation Oncology, Zhejiang Cancer HospitalAbstract Background The incidence of nasopharyngeal carcinoma (NPC) is rare, but a certain amount of mortality remains in NPC patients. Our study aimed to identify candidate genes as biomarkers for NPC screening, diagnosis, and therapy. Methods We investigated two microarray profile datasets GSE64634 and GSE12452 to screen the potential differentially expressed genes (DEGs) in NPC. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs were also performed. A protein-protein interaction (PPI) network of DEGs was constructed by STRING and visualized by Cytoscape software. The associated transcriptional factor regulatory network of the DEGs was also constructed. Results A total of 152 DEGs were identified from the GSE64634 and GSE12452 datasets, including 10 upregulated and 142 downregulated genes. Gene functional enrichment analysis indicated that these DEGs were enriched in the cilium movement, antimicrobial humoral response, O-glycan processing, mucosal immune response, carbohydrate transmembrane transporter activity, hormone biosynthetic process, neurotransmitter biosynthetic process, and drug metabolism-cytochrome P450 pathway. Five hub genes (DNALI1, RSPH4A, RSPH9, DNAI2, and ALDH3A1) and one significant module (score = 5.6) were obtained from the PPI network. Key transcriptional factors, such as SPI1, SIN3B, and GATA2, were identified with close interactions with these five hub DEGs from the gene-transcriptional factor network. Conclusions With the integrated bioinformatic analysis, numerous DEGs related to NPC were screened, and the hub DEGs we identified may be potential biomarkers for NPC.http://link.springer.com/article/10.1186/s12957-019-1605-9Nasopharyngeal carcinomaDifferentially expressed genesBioinformatic analysisTranscriptional factors |
| spellingShingle | Zhimin Ye Fangzheng Wang Fengqin Yan Lei Wang Bin Li Tongxin Liu Fujun Hu Mingxiang Jiang Weiyang Li Zhenfu Fu Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma World Journal of Surgical Oncology Nasopharyngeal carcinoma Differentially expressed genes Bioinformatic analysis Transcriptional factors |
| title | Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma |
| title_full | Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma |
| title_fullStr | Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma |
| title_full_unstemmed | Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma |
| title_short | Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma |
| title_sort | bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma |
| topic | Nasopharyngeal carcinoma Differentially expressed genes Bioinformatic analysis Transcriptional factors |
| url | http://link.springer.com/article/10.1186/s12957-019-1605-9 |
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