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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

Web interface of dbEMT.(A) The basic information in each EMT-related gene page; (B) Query interface for text search; (C) BLAST search interface for comparing query against all sequences in dbEMT; (D) Browser interface for genes in top 10 enriched pathways, top 10 enriched diseases and shared cytobands.
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f7: Web interface of dbEMT.(A) The basic information in each EMT-related gene page; (B) Query interface for text search; (C) BLAST search interface for comparing query against all sequences in dbEMT; (D) Browser interface for genes in top 10 enriched pathways, top 10 enriched diseases and shared cytobands.

Mentions: The reliable open source relational database MySQL was used to store all the data and annotations in dbEMT on a Linux server. The CGI Web-based interface to the database is implemented using Perl. Using the Perl CGI module and JavaScript technology, web pages for each gene in the database are generated. In dbEMT, all the genes are annotated comprehensively with hyperlinks to their original data resources (Fig. 7A). Gene expression in various normal tissues and cancer samples are represented in a colored bar chart (Fig. 5A). In addition, the extensive literature evidence associated with EMT genes are also complied and highlighted with keywords related to EMT or diseases.


dbEMT: an epithelial-mesenchymal transition associated gene resource.

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

Web interface of dbEMT.(A) The basic information in each EMT-related gene page; (B) Query interface for text search; (C) BLAST search interface for comparing query against all sequences in dbEMT; (D) Browser interface for genes in top 10 enriched pathways, top 10 enriched diseases and shared cytobands.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f7: Web interface of dbEMT.(A) The basic information in each EMT-related gene page; (B) Query interface for text search; (C) BLAST search interface for comparing query against all sequences in dbEMT; (D) Browser interface for genes in top 10 enriched pathways, top 10 enriched diseases and shared cytobands.
Mentions: The reliable open source relational database MySQL was used to store all the data and annotations in dbEMT on a Linux server. The CGI Web-based interface to the database is implemented using Perl. Using the Perl CGI module and JavaScript technology, web pages for each gene in the database are generated. In dbEMT, all the genes are annotated comprehensively with hyperlinks to their original data resources (Fig. 7A). Gene expression in various normal tissues and cancer samples are represented in a colored bar chart (Fig. 5A). In addition, the extensive literature evidence associated with EMT genes are also complied and highlighted with keywords related to EMT or diseases.

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