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Identification of differentially expressed genes between lung adenocarcinoma and lung squamous cell carcinoma by gene expression profiling.

Lu C, Chen H, Shan Z, Yang L - Mol Med Rep (2016)

Bottom Line: Subsequently, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery, and a global network was constructed.However, the DEGs in the lung adenocarcinoma group were not significantly enriched in any specific pathway.Subsequently, a global network of lung cancer was constructed, which consisted of 341 genes and 1,569 edges, of which the top five genes were HSP90AA1, BCL2, CDK2, KIT and HDAC2.

View Article: PubMed Central - PubMed

Affiliation: Department of Thoracic Surgery, Changhai Hospital, Shanghai 200433, P.R. China.

ABSTRACT
The present study aimed to identify the differentially expressed genes (DEGs) between lung adenocarcinoma and normal lung tissues, and between lung squamous cell carcinoma and normal lung tissues, with the purpose of identifying potential biomarkers for the treatment of lung cancer. The gene expression profile (GSE6044) was downloaded from the Gene Expression Omnibus database, which included data from 10 lung adenocarcinoma samples, 10 lung squamous cell carcinoma samples, and five matched normal lung tissue samples. After data processing, DEGs were identified using the Student's t‑test adjusted via the Benjamini‑Hochberg method. Subsequently, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery, and a global network was constructed. A total of 95 upregulated and 241 downregulated DEGs were detected in lung adenocarcinoma samples, and 204 upregulated and 285 downregulated DEGs were detected in lung squamous cell carcinoma samples, as compared with the normal lung tissue samples. The DEGs in the lung squamous cell carcinoma group were enriched in the following three pathways: Hsa04110, Cell cycle; hsa03030, DNA replication; and hsa03430, mismatch repair. However, the DEGs in the lung adenocarcinoma group were not significantly enriched in any specific pathway. Subsequently, a global network of lung cancer was constructed, which consisted of 341 genes and 1,569 edges, of which the top five genes were HSP90AA1, BCL2, CDK2, KIT and HDAC2. The expression trends of the above genes were different in lung adenocarcinoma and lung squamous cell carcinoma when compared with normal tissues. Therefore, these genes were suggested to be crucial genes for differentiating lung adenocarcinoma and lung squamous cell carcinoma.

No MeSH data available.


Related in: MedlinePlus

Global network of cancer-associated genes. Cancer network of lung squamous cell carcinoma samples. Red dots represent upregulated genes; green dots represent downregulated genes. The depth of color represents the extent of the fold change.
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f2-mmr-14-02-1483: Global network of cancer-associated genes. Cancer network of lung squamous cell carcinoma samples. Red dots represent upregulated genes; green dots represent downregulated genes. The depth of color represents the extent of the fold change.

Mentions: Two upregulated DEGs and seven downregulated DEGs in the adenocarcinoma group, and eight upregulated DEGs and five downregulated DEGs in the squamous cell carcinoma group were selected in the global network under the FDR<0.1 and FC >1.5 or <0.67 criteria. These DEGs were used to construct the PPI network based on the HRPD database; the network consisted of 21 DEGs and 517 relationships with two common genes, NKX3-1 and MAPK10) in Fig. 2A and B. The degrees (number of interacting partners) of the genes in the PPI networks were calculated (Table I), and the top five genes were identified, as follows: HSP90AA1, BCL2, CDK2, KIT and HDAC2, which had degrees of 81, 64, 63, 50 and 46, respectively (Table II). HSP90AA1 exhibited the highest degree, and was the most downregulated gene detected in the adenocarcinoma group. Furthermore, the expression differences of these 19 DEGs were compared between the two types of lung cancer (Table II). The results demonstrated that some genes exhibited similar expression trends between the groups, such as NKX3-1 and MAPK10, whereas DVL3 was upregulated in squamous cell carcinoma samples; however, its expression was not significantly altered in adenocarcinoma samples. The expression of BCL2 was significantly downregulated in adenocarcinoma samples, but not changed in squamous cell carcinoma samples.


Identification of differentially expressed genes between lung adenocarcinoma and lung squamous cell carcinoma by gene expression profiling.

Lu C, Chen H, Shan Z, Yang L - Mol Med Rep (2016)

Global network of cancer-associated genes. Cancer network of lung squamous cell carcinoma samples. Red dots represent upregulated genes; green dots represent downregulated genes. The depth of color represents the extent of the fold change.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940109&req=5

f2-mmr-14-02-1483: Global network of cancer-associated genes. Cancer network of lung squamous cell carcinoma samples. Red dots represent upregulated genes; green dots represent downregulated genes. The depth of color represents the extent of the fold change.
Mentions: Two upregulated DEGs and seven downregulated DEGs in the adenocarcinoma group, and eight upregulated DEGs and five downregulated DEGs in the squamous cell carcinoma group were selected in the global network under the FDR<0.1 and FC >1.5 or <0.67 criteria. These DEGs were used to construct the PPI network based on the HRPD database; the network consisted of 21 DEGs and 517 relationships with two common genes, NKX3-1 and MAPK10) in Fig. 2A and B. The degrees (number of interacting partners) of the genes in the PPI networks were calculated (Table I), and the top five genes were identified, as follows: HSP90AA1, BCL2, CDK2, KIT and HDAC2, which had degrees of 81, 64, 63, 50 and 46, respectively (Table II). HSP90AA1 exhibited the highest degree, and was the most downregulated gene detected in the adenocarcinoma group. Furthermore, the expression differences of these 19 DEGs were compared between the two types of lung cancer (Table II). The results demonstrated that some genes exhibited similar expression trends between the groups, such as NKX3-1 and MAPK10, whereas DVL3 was upregulated in squamous cell carcinoma samples; however, its expression was not significantly altered in adenocarcinoma samples. The expression of BCL2 was significantly downregulated in adenocarcinoma samples, but not changed in squamous cell carcinoma samples.

Bottom Line: Subsequently, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery, and a global network was constructed.However, the DEGs in the lung adenocarcinoma group were not significantly enriched in any specific pathway.Subsequently, a global network of lung cancer was constructed, which consisted of 341 genes and 1,569 edges, of which the top five genes were HSP90AA1, BCL2, CDK2, KIT and HDAC2.

View Article: PubMed Central - PubMed

Affiliation: Department of Thoracic Surgery, Changhai Hospital, Shanghai 200433, P.R. China.

ABSTRACT
The present study aimed to identify the differentially expressed genes (DEGs) between lung adenocarcinoma and normal lung tissues, and between lung squamous cell carcinoma and normal lung tissues, with the purpose of identifying potential biomarkers for the treatment of lung cancer. The gene expression profile (GSE6044) was downloaded from the Gene Expression Omnibus database, which included data from 10 lung adenocarcinoma samples, 10 lung squamous cell carcinoma samples, and five matched normal lung tissue samples. After data processing, DEGs were identified using the Student's t‑test adjusted via the Benjamini‑Hochberg method. Subsequently, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery, and a global network was constructed. A total of 95 upregulated and 241 downregulated DEGs were detected in lung adenocarcinoma samples, and 204 upregulated and 285 downregulated DEGs were detected in lung squamous cell carcinoma samples, as compared with the normal lung tissue samples. The DEGs in the lung squamous cell carcinoma group were enriched in the following three pathways: Hsa04110, Cell cycle; hsa03030, DNA replication; and hsa03430, mismatch repair. However, the DEGs in the lung adenocarcinoma group were not significantly enriched in any specific pathway. Subsequently, a global network of lung cancer was constructed, which consisted of 341 genes and 1,569 edges, of which the top five genes were HSP90AA1, BCL2, CDK2, KIT and HDAC2. The expression trends of the above genes were different in lung adenocarcinoma and lung squamous cell carcinoma when compared with normal tissues. Therefore, these genes were suggested to be crucial genes for differentiating lung adenocarcinoma and lung squamous cell carcinoma.

No MeSH data available.


Related in: MedlinePlus