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Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods
The molecular mechanism of the occurrence and development of papillary thyroid carcinoma (PTC) has been widely explored, but has not been completely elucidated. The present study aimed to identify and analyze genes associated with PTC by bioinformatics methods. Two independent datasets were download...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Portland Press Ltd.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443946/ https://www.ncbi.nlm.nih.gov/pubmed/30872410 http://dx.doi.org/10.1042/BSR20190083 |
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author | Zhang, Shulong Wang, Quan Han, Qi Han, Huazhong Lu, Pinxiang |
author_facet | Zhang, Shulong Wang, Quan Han, Qi Han, Huazhong Lu, Pinxiang |
author_sort | Zhang, Shulong |
collection | PubMed |
description | The molecular mechanism of the occurrence and development of papillary thyroid carcinoma (PTC) has been widely explored, but has not been completely elucidated. The present study aimed to identify and analyze genes associated with PTC by bioinformatics methods. Two independent datasets were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between PTC tissues and matched non-cancerous tissues were identified using GEO2R tool. The common DEGs in the two datasets were screened out by VennDiagram package, and analyzed by the following tools: KOBAS, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Search tool for the retrieval of interacting genes/proteins (STRING), UALCAN and Gene expression profiling interactive analysis (GEPIA). A total of 513 common DEGs, including 259 common up-regulated and 254 common down-regulated genes in PTC, were screened out. These common up-regulated and down-regulated DEGs were most significantly enriched in cytokine–cytokine receptor interaction and metabolic pathways, respectively. Protein–protein interactions (PPI) network analysis showed that the up-regulated genes: FN1, SDC4, NMU, LPAR5 and the down-regulated genes: BCL2 and CXCL12 were key genes. Survival analysis indicated that the high expression of FN1 and NMU genes significantly decreased disease-free survival of patients with thyroid carcinoma. In conclusion, the genes and pathways identified in the current study will not only contribute to elucidating the pathogenesis of PTC, but also provide prognostic markers and therapeutic targets for PTC. |
format | Online Article Text |
id | pubmed-6443946 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Portland Press Ltd. |
record_format | MEDLINE/PubMed |
spelling | pubmed-64439462019-04-16 Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods Zhang, Shulong Wang, Quan Han, Qi Han, Huazhong Lu, Pinxiang Biosci Rep Research Articles The molecular mechanism of the occurrence and development of papillary thyroid carcinoma (PTC) has been widely explored, but has not been completely elucidated. The present study aimed to identify and analyze genes associated with PTC by bioinformatics methods. Two independent datasets were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between PTC tissues and matched non-cancerous tissues were identified using GEO2R tool. The common DEGs in the two datasets were screened out by VennDiagram package, and analyzed by the following tools: KOBAS, Database for Annotation, Visualization, and Integrated Discovery (DAVID), Search tool for the retrieval of interacting genes/proteins (STRING), UALCAN and Gene expression profiling interactive analysis (GEPIA). A total of 513 common DEGs, including 259 common up-regulated and 254 common down-regulated genes in PTC, were screened out. These common up-regulated and down-regulated DEGs were most significantly enriched in cytokine–cytokine receptor interaction and metabolic pathways, respectively. Protein–protein interactions (PPI) network analysis showed that the up-regulated genes: FN1, SDC4, NMU, LPAR5 and the down-regulated genes: BCL2 and CXCL12 were key genes. Survival analysis indicated that the high expression of FN1 and NMU genes significantly decreased disease-free survival of patients with thyroid carcinoma. In conclusion, the genes and pathways identified in the current study will not only contribute to elucidating the pathogenesis of PTC, but also provide prognostic markers and therapeutic targets for PTC. Portland Press Ltd. 2019-04-02 /pmc/articles/PMC6443946/ /pubmed/30872410 http://dx.doi.org/10.1042/BSR20190083 Text en © 2019 The Author(s). http://creativecommons.org/licenses/by/4.0/This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) (http://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Articles Zhang, Shulong Wang, Quan Han, Qi Han, Huazhong Lu, Pinxiang Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods |
title | Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods |
title_full | Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods |
title_fullStr | Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods |
title_full_unstemmed | Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods |
title_short | Identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods |
title_sort | identification and analysis of genes associated with papillary thyroid carcinoma by bioinformatics methods |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443946/ https://www.ncbi.nlm.nih.gov/pubmed/30872410 http://dx.doi.org/10.1042/BSR20190083 |
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