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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

Pipeline for collection, expansion and annotation of EMT-related genes.
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f6: Pipeline for collection, expansion and annotation of EMT-related genes.

Mentions: To obtain a precise EMT-related gene list with experimental evidence, we performed our literature search and curation as the following four steps (Fig. 6). Firstly, we first performed an extensive literature query against PubMed (on Dec 19th, 2013) using complex expression: ("Epithelial-mesenchymal transition"[Title/Abstract] OR "Epithelial mesenchymal transition"[Title/Abstract] OR "EMT"[Title/Abstract]) AND (("genome-wide association study" [Title/Abstract] OR "genome wide association study" [Title/Abstract]) OR ("gene"[Title/Abstract] AND ("association"[Title/Abstract] OR "microarray" [Title/Abstract] OR "expression" [Title/Abstract] OR "linkage" [Title/Abstract] OR "proteomics" [Title/Abstract] OR "genetic" [Title/Abstract] OR "metabolomics" [Title/Abstract] OR "copy number variation" [Title/Abstract] OR "idiopathic" [Title/Abstract] OR "hereditable" [Title/Abstract] OR "family" [Title/Abstract] OR "mouse model" [Title/Abstract] OR "animal model" [Title/Abstract] OR "microRNA" [Title/Abstract] OR "mutation" [Title/Abstract] OR "SNP" [Title/Abstract] OR "drug" [Title/Abstract] OR "transporter" [Title/Abstract]))). Secondly, 1507 abstracts were retrieved and grouped by the “Related Articles” function in Entrez system. Thirdly, we then extracted the EMT-related description from the grouped abstracts. Those sentences related to EMT were manually read to extract the gene names and organism information with experimental evidence. Lastly, the extracted candidate gene name and organism information were manually checked. Finally, the 377 Entrez human Gene IDs with high confidence were collected as core EMT-related genes. This core gene list will be regularly updated based on newly published literature.


dbEMT: an epithelial-mesenchymal transition associated gene resource.

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

Pipeline for collection, expansion and annotation of EMT-related genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Pipeline for collection, expansion and annotation of EMT-related genes.
Mentions: To obtain a precise EMT-related gene list with experimental evidence, we performed our literature search and curation as the following four steps (Fig. 6). Firstly, we first performed an extensive literature query against PubMed (on Dec 19th, 2013) using complex expression: ("Epithelial-mesenchymal transition"[Title/Abstract] OR "Epithelial mesenchymal transition"[Title/Abstract] OR "EMT"[Title/Abstract]) AND (("genome-wide association study" [Title/Abstract] OR "genome wide association study" [Title/Abstract]) OR ("gene"[Title/Abstract] AND ("association"[Title/Abstract] OR "microarray" [Title/Abstract] OR "expression" [Title/Abstract] OR "linkage" [Title/Abstract] OR "proteomics" [Title/Abstract] OR "genetic" [Title/Abstract] OR "metabolomics" [Title/Abstract] OR "copy number variation" [Title/Abstract] OR "idiopathic" [Title/Abstract] OR "hereditable" [Title/Abstract] OR "family" [Title/Abstract] OR "mouse model" [Title/Abstract] OR "animal model" [Title/Abstract] OR "microRNA" [Title/Abstract] OR "mutation" [Title/Abstract] OR "SNP" [Title/Abstract] OR "drug" [Title/Abstract] OR "transporter" [Title/Abstract]))). Secondly, 1507 abstracts were retrieved and grouped by the “Related Articles” function in Entrez system. Thirdly, we then extracted the EMT-related description from the grouped abstracts. Those sentences related to EMT were manually read to extract the gene names and organism information with experimental evidence. Lastly, the extracted candidate gene name and organism information were manually checked. Finally, the 377 Entrez human Gene IDs with high confidence were collected as core EMT-related genes. This core gene list will be regularly updated based on newly published literature.

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