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dbEMT: an epithelial-mesenchymal transition associated gene resource.

Zhao M, Kong L, Liu Y, Qu H - Sci Rep (2015)

Bottom Line: In addition, the disease enrichment analysis provides a clue for the potential transformation in affected tissues or cells in Alzheimer's disease and Type 2 Diabetes.Our further reconstruction of the EMT-related protein-protein interaction network uncovered a highly modular structure.These results illustrate the importance of dbEMT to our understanding of cell development and cancer metastasis, and also highlight the utility of dbEMT for elucidating the functions of EMT-related genes.

View Article: PubMed Central - PubMed

Affiliation: School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.

ABSTRACT
As a cellular process that changes epithelial cells to mesenchymal cells, Epithelial-mesenchymal transition (EMT) plays important roles in development and cancer metastasis. Recent studies on cancer metastasis have identified many new susceptibility genes that control this transition. However, there is no comprehensive resource for EMT by integrating various genetic studies and the relationship between EMT and the risk of complex diseases such as cancer are still unclear. To investigate the cellular complexity of EMT, we have constructed dbEMT (http://dbemt.bioinfo-minzhao.org/), the first literature-based gene resource for exploring EMT-related human genes. We manually curated 377 experimentally verified genes from literature. Functional analyses highlighted the prominent role of proteoglycans in tumor metastatic cascades. In addition, the disease enrichment analysis provides a clue for the potential transformation in affected tissues or cells in Alzheimer's disease and Type 2 Diabetes. Moreover, the global mutation pattern of EMT-related genes across multiple cancers may reveal common cancer metastasis mechanisms. Our further reconstruction of the EMT-related protein-protein interaction network uncovered a highly modular structure. These results illustrate the importance of dbEMT to our understanding of cell development and cancer metastasis, and also highlight the utility of dbEMT for elucidating the functions of EMT-related genes.

No MeSH data available.


Related in: MedlinePlus

The heatmap for the 35 genes whose expression are increasing from stage III to stage IV in TCGA ovarian cancer samples.
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f4: The heatmap for the 35 genes whose expression are increasing from stage III to stage IV in TCGA ovarian cancer samples.

Mentions: As the EMT often occurs during the cancer metastasis, we only extracted those ovarian cancer samples related to stage III to stage IV, where metastasis transition occurs. The aim of this analysis was to identify those EMT-related genes whose expression is increasing between Stage III to stage IV. As shown in the Fig. 4, there are 35 mutated genes having comparatively high expression in average in ovarian cancer (student t test, P-values < 0.05). Multiple genes (MUC1615, POSTN16) have been reported to be related to ovarian cancer metastasis or cell movement. Our analysis reveals a similar relationship between periostin (POSTN) and EMT of ovarian cancer. Some of genes (e.g. MMP7) were reported to have potential biomarker role in ovarian cancer, but not for EMT process17. Those genes might be used as biomarkers for the ovarian cancer EMT-related process, especially, the strong different expression of periostin from stage III to IV which may indicate the ovarian cancer EMT process.


dbEMT: an epithelial-mesenchymal transition associated gene resource.

Zhao M, Kong L, Liu Y, Qu H - Sci Rep (2015)

The heatmap for the 35 genes whose expression are increasing from stage III to stage IV in TCGA ovarian cancer samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4477208&req=5

f4: The heatmap for the 35 genes whose expression are increasing from stage III to stage IV in TCGA ovarian cancer samples.
Mentions: As the EMT often occurs during the cancer metastasis, we only extracted those ovarian cancer samples related to stage III to stage IV, where metastasis transition occurs. The aim of this analysis was to identify those EMT-related genes whose expression is increasing between Stage III to stage IV. As shown in the Fig. 4, there are 35 mutated genes having comparatively high expression in average in ovarian cancer (student t test, P-values < 0.05). Multiple genes (MUC1615, POSTN16) have been reported to be related to ovarian cancer metastasis or cell movement. Our analysis reveals a similar relationship between periostin (POSTN) and EMT of ovarian cancer. Some of genes (e.g. MMP7) were reported to have potential biomarker role in ovarian cancer, but not for EMT process17. Those genes might be used as biomarkers for the ovarian cancer EMT-related process, especially, the strong different expression of periostin from stage III to IV which may indicate the ovarian cancer EMT process.

Bottom Line: In addition, the disease enrichment analysis provides a clue for the potential transformation in affected tissues or cells in Alzheimer's disease and Type 2 Diabetes.Our further reconstruction of the EMT-related protein-protein interaction network uncovered a highly modular structure.These results illustrate the importance of dbEMT to our understanding of cell development and cancer metastasis, and also highlight the utility of dbEMT for elucidating the functions of EMT-related genes.

View Article: PubMed Central - PubMed

Affiliation: School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia.

ABSTRACT
As a cellular process that changes epithelial cells to mesenchymal cells, Epithelial-mesenchymal transition (EMT) plays important roles in development and cancer metastasis. Recent studies on cancer metastasis have identified many new susceptibility genes that control this transition. However, there is no comprehensive resource for EMT by integrating various genetic studies and the relationship between EMT and the risk of complex diseases such as cancer are still unclear. To investigate the cellular complexity of EMT, we have constructed dbEMT (http://dbemt.bioinfo-minzhao.org/), the first literature-based gene resource for exploring EMT-related human genes. We manually curated 377 experimentally verified genes from literature. Functional analyses highlighted the prominent role of proteoglycans in tumor metastatic cascades. In addition, the disease enrichment analysis provides a clue for the potential transformation in affected tissues or cells in Alzheimer's disease and Type 2 Diabetes. Moreover, the global mutation pattern of EMT-related genes across multiple cancers may reveal common cancer metastasis mechanisms. Our further reconstruction of the EMT-related protein-protein interaction network uncovered a highly modular structure. These results illustrate the importance of dbEMT to our understanding of cell development and cancer metastasis, and also highlight the utility of dbEMT for elucidating the functions of EMT-related genes.

No MeSH data available.


Related in: MedlinePlus