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Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach.

Liu JL, Wang TS - PLoS ONE (2015)

Bottom Line: Decidualization is a crucial process for successful embryo implantation and pregnancy in humans.We prioritized genes in this network and identified 12 genes that may be key regulators of decidualization.These findings would provide some clues for further research on the mechanism underlying decidualization.

View Article: PubMed Central - PubMed

Affiliation: College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.

ABSTRACT
Decidualization is a crucial process for successful embryo implantation and pregnancy in humans. Defects in decidualization during early pregnancy are associated with several pregnancy complications, such as pre-eclampsia, intrauterine growth restriction and recurrent pregnancy loss. However, the mechanism underlying decidualization remains poorly understood. In the present study, we performed a systematic analysis of decidualization-related genes using text mining. We identified 286 genes for humans and 287 genes for mice respectively, with an overlap of 111 genes shared by both species. Through enrichment test, we demonstrated that although divergence was observed, the majority of enriched gene ontology terms and pathways were shared by both species, suggesting that functional categories were more conserved than individual genes. We further constructed a decidualization-related protein-protein interaction network consisted of 344 nodes connected via 1,541 edges. We prioritized genes in this network and identified 12 genes that may be key regulators of decidualization. These findings would provide some clues for further research on the mechanism underlying decidualization.

No MeSH data available.


Related in: MedlinePlus

Gene ontology (GO) enrichment analysis of decidualization-related genes.(A) The union of human and mouse gene sets were analyzed using BiNGO software. Significantly enriched GOslim categories were highlighted with different colors representing different levels of significance. The size of each circle is correlated to the number of genes. (B) Comparative GO enrichment analysis for species-specific gene sets arranged in the biological process category (BP), the cellular component category (CC) and the molecular function category (MF), respectively. The analysis was applied to human and mouse gene sets, as well as 4 additional gene sets generated by set operations (union, intersection and difference) between them. The columns represent different gene sets, while the rows represent statistically significant GO terms.
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pone.0134585.g002: Gene ontology (GO) enrichment analysis of decidualization-related genes.(A) The union of human and mouse gene sets were analyzed using BiNGO software. Significantly enriched GOslim categories were highlighted with different colors representing different levels of significance. The size of each circle is correlated to the number of genes. (B) Comparative GO enrichment analysis for species-specific gene sets arranged in the biological process category (BP), the cellular component category (CC) and the molecular function category (MF), respectively. The analysis was applied to human and mouse gene sets, as well as 4 additional gene sets generated by set operations (union, intersection and difference) between them. The columns represent different gene sets, while the rows represent statistically significant GO terms.

Mentions: All 462 decidualization-related genes (286 genes for humans and 287 genes for mice) were functionally categorized based on gene ontology (GO) annotation terms using BiNGO software. Enrichment analysis revealed that a total of 17 GO terms exhibited significance as overrepresented terms (p < 0.05). In the biological process category, 7 GO terms, namely cell communication, response to stimulus, development, cell death, cell motility, cell differentiation and metabolic process, were found to be significantly enriched. GO terms related to extracellular region, cell surface and membrane were significantly enriched under the cellular component category. Enriched GO terms in the molecular function category were transcription regulator activity, antioxidant activity, hydrolase activity, binding, receptor activity, signal transducer activity and protein binding. The hierarchical organization of these GO terms is shown in Fig 2A, together with the significance of enrichment indicated by different colors.


Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach.

Liu JL, Wang TS - PLoS ONE (2015)

Gene ontology (GO) enrichment analysis of decidualization-related genes.(A) The union of human and mouse gene sets were analyzed using BiNGO software. Significantly enriched GOslim categories were highlighted with different colors representing different levels of significance. The size of each circle is correlated to the number of genes. (B) Comparative GO enrichment analysis for species-specific gene sets arranged in the biological process category (BP), the cellular component category (CC) and the molecular function category (MF), respectively. The analysis was applied to human and mouse gene sets, as well as 4 additional gene sets generated by set operations (union, intersection and difference) between them. The columns represent different gene sets, while the rows represent statistically significant GO terms.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4519252&req=5

pone.0134585.g002: Gene ontology (GO) enrichment analysis of decidualization-related genes.(A) The union of human and mouse gene sets were analyzed using BiNGO software. Significantly enriched GOslim categories were highlighted with different colors representing different levels of significance. The size of each circle is correlated to the number of genes. (B) Comparative GO enrichment analysis for species-specific gene sets arranged in the biological process category (BP), the cellular component category (CC) and the molecular function category (MF), respectively. The analysis was applied to human and mouse gene sets, as well as 4 additional gene sets generated by set operations (union, intersection and difference) between them. The columns represent different gene sets, while the rows represent statistically significant GO terms.
Mentions: All 462 decidualization-related genes (286 genes for humans and 287 genes for mice) were functionally categorized based on gene ontology (GO) annotation terms using BiNGO software. Enrichment analysis revealed that a total of 17 GO terms exhibited significance as overrepresented terms (p < 0.05). In the biological process category, 7 GO terms, namely cell communication, response to stimulus, development, cell death, cell motility, cell differentiation and metabolic process, were found to be significantly enriched. GO terms related to extracellular region, cell surface and membrane were significantly enriched under the cellular component category. Enriched GO terms in the molecular function category were transcription regulator activity, antioxidant activity, hydrolase activity, binding, receptor activity, signal transducer activity and protein binding. The hierarchical organization of these GO terms is shown in Fig 2A, together with the significance of enrichment indicated by different colors.

Bottom Line: Decidualization is a crucial process for successful embryo implantation and pregnancy in humans.We prioritized genes in this network and identified 12 genes that may be key regulators of decidualization.These findings would provide some clues for further research on the mechanism underlying decidualization.

View Article: PubMed Central - PubMed

Affiliation: College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.

ABSTRACT
Decidualization is a crucial process for successful embryo implantation and pregnancy in humans. Defects in decidualization during early pregnancy are associated with several pregnancy complications, such as pre-eclampsia, intrauterine growth restriction and recurrent pregnancy loss. However, the mechanism underlying decidualization remains poorly understood. In the present study, we performed a systematic analysis of decidualization-related genes using text mining. We identified 286 genes for humans and 287 genes for mice respectively, with an overlap of 111 genes shared by both species. Through enrichment test, we demonstrated that although divergence was observed, the majority of enriched gene ontology terms and pathways were shared by both species, suggesting that functional categories were more conserved than individual genes. We further constructed a decidualization-related protein-protein interaction network consisted of 344 nodes connected via 1,541 edges. We prioritized genes in this network and identified 12 genes that may be key regulators of decidualization. These findings would provide some clues for further research on the mechanism underlying decidualization.

No MeSH data available.


Related in: MedlinePlus