Limits...
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 mutational landscape for the top 100 EMT-related genes in multiple cancers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4477208&req=5

f2: The mutational landscape for the top 100 EMT-related genes in multiple cancers.

Mentions: Although EMT-related genes have been demonstrated to have abnormal gene expression or other functional relevance to cancer, the systematic examination of the genetic variants has not been conducted. These are useful for users to identify potential cancer metastasis genes for further screening. As shown in Fig. 2, the top 100 ranking EMT-related genes have tremendous mutations in cancers. It is interesting that the 100 genes are 98.9% mutated in both head/neck carcinomas (276 individuals) and lung squamous cell carcinomas (176 individuals). In 234 uterine cancer samples, there were more single nucleotide mutations for the patients. The most striking point is that 95.2% of the lung squamous cell carcinoma population from an analysis of 40 patients at the Johns Hopkins . with only single nucleotide mutations. The same observation can be found in colorectal cancer from the Genentech dataset (90.3% in 65 individuals) and esophagus cancer (88.4% in 129 individuals). In contrast, the three studies on medulloblastoma (MBL) only show less than 20% of mutation frequency in the designed case population. This suggests that MBL may have distinct metastasis mechanisms that are different from other cancers.


dbEMT: an epithelial-mesenchymal transition associated gene resource.

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

The mutational landscape for the top 100 EMT-related genes in multiple cancers.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: The mutational landscape for the top 100 EMT-related genes in multiple cancers.
Mentions: Although EMT-related genes have been demonstrated to have abnormal gene expression or other functional relevance to cancer, the systematic examination of the genetic variants has not been conducted. These are useful for users to identify potential cancer metastasis genes for further screening. As shown in Fig. 2, the top 100 ranking EMT-related genes have tremendous mutations in cancers. It is interesting that the 100 genes are 98.9% mutated in both head/neck carcinomas (276 individuals) and lung squamous cell carcinomas (176 individuals). In 234 uterine cancer samples, there were more single nucleotide mutations for the patients. The most striking point is that 95.2% of the lung squamous cell carcinoma population from an analysis of 40 patients at the Johns Hopkins . with only single nucleotide mutations. The same observation can be found in colorectal cancer from the Genentech dataset (90.3% in 65 individuals) and esophagus cancer (88.4% in 129 individuals). In contrast, the three studies on medulloblastoma (MBL) only show less than 20% of mutation frequency in the designed case population. This suggests that MBL may have distinct metastasis mechanisms that are different from other cancers.

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