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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 highlighted mutated EMT-related genes in colorectal and pancreatic cancers.(a) The KEGG signaling map for colorectal cancer; (b) The KEGG signaling map for pancreatic cancer. The genes with pink color in two maps are detected in our dbEMT; the remaining green genes are human genes not in our dbEMT."
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f1: The highlighted mutated EMT-related genes in colorectal and pancreatic cancers.(a) The KEGG signaling map for colorectal cancer; (b) The KEGG signaling map for pancreatic cancer. The genes with pink color in two maps are detected in our dbEMT; the remaining green genes are human genes not in our dbEMT."

Mentions: As a fundamental role on cell destination, it is not surprising that the EMT-related genes are consistently related to a number of complex diseases. However, the enrichment analysis of an EMT-related gene does not reveal if EMT has contributed to a specific disease. It does allow to test the risk factor of EMT in relevant diseases. The enrichment analysis on a few disease-related databases has confirmed that the 377 genes are related to a broad-spectrum of human cancers such as (Table 2). In total, 277 genes are related to various cancers. The cancers mainly occur in the digestive and urinary systems, including colorectal, pancreatic, endometrial, prostate, bladder, melanoma, renal cell, thyroid, oral, gastric, ovary, leukemia, cholangiocarcinoma, choriocarcinoma. Although many reports suggest that EMT is associated with cancer invasion and metastasis, there is no comparison of EMT across cancers. It is possible that the underlying common molecular mechanism between EMT and any cancers are the same. As shown in Fig. 1, there are 27 EMT-related genes in both colorectal cancer and pancreatic cancer. However, only 18 of these are common to both: SMAD2, SMAD3, SMAD4, PIK3CA, MAP2K1, TP53, AKT1, BRAF, TGFBR1, RAF1, TGFB3, TGFB2, MAPK3, MAPK1, MAPK8, KRAS, RAC1, TGFB1.


dbEMT: an epithelial-mesenchymal transition associated gene resource.

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

The highlighted mutated EMT-related genes in colorectal and pancreatic cancers.(a) The KEGG signaling map for colorectal cancer; (b) The KEGG signaling map for pancreatic cancer. The genes with pink color in two maps are detected in our dbEMT; the remaining green genes are human genes not in our dbEMT."
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: The highlighted mutated EMT-related genes in colorectal and pancreatic cancers.(a) The KEGG signaling map for colorectal cancer; (b) The KEGG signaling map for pancreatic cancer. The genes with pink color in two maps are detected in our dbEMT; the remaining green genes are human genes not in our dbEMT."
Mentions: As a fundamental role on cell destination, it is not surprising that the EMT-related genes are consistently related to a number of complex diseases. However, the enrichment analysis of an EMT-related gene does not reveal if EMT has contributed to a specific disease. It does allow to test the risk factor of EMT in relevant diseases. The enrichment analysis on a few disease-related databases has confirmed that the 377 genes are related to a broad-spectrum of human cancers such as (Table 2). In total, 277 genes are related to various cancers. The cancers mainly occur in the digestive and urinary systems, including colorectal, pancreatic, endometrial, prostate, bladder, melanoma, renal cell, thyroid, oral, gastric, ovary, leukemia, cholangiocarcinoma, choriocarcinoma. Although many reports suggest that EMT is associated with cancer invasion and metastasis, there is no comparison of EMT across cancers. It is possible that the underlying common molecular mechanism between EMT and any cancers are the same. As shown in Fig. 1, there are 27 EMT-related genes in both colorectal cancer and pancreatic cancer. However, only 18 of these are common to both: SMAD2, SMAD3, SMAD4, PIK3CA, MAP2K1, TP53, AKT1, BRAF, TGFBR1, RAF1, TGFB3, TGFB2, MAPK3, MAPK1, MAPK8, KRAS, RAC1, TGFB1.

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