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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

Pathway enrichment analysis of decidualization-related genes.(A) The figure shows the significantly enriched pathways identified by using DAVID online tools. The bars represent the enrichment p-value at logarithmic scale. (B) Visualization of the LIF-STAT signaling pathway. Nodes represent genes. The node color indicates the status of the gene as specific to human (red), specific to mouse (green), or shared by both (blue). Edges represent gene dependences derived from KEGG pathway database. Genes without a direct interaction with others are not included. This graph is generated using the Cytoscape software.
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pone.0134585.g003: Pathway enrichment analysis of decidualization-related genes.(A) The figure shows the significantly enriched pathways identified by using DAVID online tools. The bars represent the enrichment p-value at logarithmic scale. (B) Visualization of the LIF-STAT signaling pathway. Nodes represent genes. The node color indicates the status of the gene as specific to human (red), specific to mouse (green), or shared by both (blue). Edges represent gene dependences derived from KEGG pathway database. Genes without a direct interaction with others are not included. This graph is generated using the Cytoscape software.

Mentions: In addition to GO analysis, we also performed pathway analysis by using DAVID online tools. Unlike GO, which only contains gene lists for different functional categories, pathway database also stores the information of gene dependencies in each pathway. In the present study, all decidualization-related genes were mapped to KEGG pathways. A total of 5 pathways, namely Jak-STAT signaling pathway, ErbB signaling pathway, focal adhesion, apoptosis and MAPK signaling pathway, were significantly enriched in both human and mouse gene sets (p < 0.05) (Fig 3A). The enrichment of VEGF signaling pathway, renin-angiotensin system, Toll-like receptor signaling pathway and GnRH signaling pathway was unique to the human gene set, whereas TGF-beta signaling pathway, p53 signaling pathway, Wnt signaling pathway, Hedgehog signaling pathway and cell cycle was enriched only in the mouse gene set (Fig 3A). Based on enrichment p-values, the most highly overrepresented pathway went to the LIF-STAT pathway. In this pathway, we identified 18 genes, of which 6 are specific to humans, 4 are specific to mice, and 8 are shared by both (Fig 3B). The LIF-STAT pathway is known to play an important role during decidualization in both humans [31] and mice [32–34].


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

Liu JL, Wang TS - PLoS ONE (2015)

Pathway enrichment analysis of decidualization-related genes.(A) The figure shows the significantly enriched pathways identified by using DAVID online tools. The bars represent the enrichment p-value at logarithmic scale. (B) Visualization of the LIF-STAT signaling pathway. Nodes represent genes. The node color indicates the status of the gene as specific to human (red), specific to mouse (green), or shared by both (blue). Edges represent gene dependences derived from KEGG pathway database. Genes without a direct interaction with others are not included. This graph is generated using the Cytoscape software.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134585.g003: Pathway enrichment analysis of decidualization-related genes.(A) The figure shows the significantly enriched pathways identified by using DAVID online tools. The bars represent the enrichment p-value at logarithmic scale. (B) Visualization of the LIF-STAT signaling pathway. Nodes represent genes. The node color indicates the status of the gene as specific to human (red), specific to mouse (green), or shared by both (blue). Edges represent gene dependences derived from KEGG pathway database. Genes without a direct interaction with others are not included. This graph is generated using the Cytoscape software.
Mentions: In addition to GO analysis, we also performed pathway analysis by using DAVID online tools. Unlike GO, which only contains gene lists for different functional categories, pathway database also stores the information of gene dependencies in each pathway. In the present study, all decidualization-related genes were mapped to KEGG pathways. A total of 5 pathways, namely Jak-STAT signaling pathway, ErbB signaling pathway, focal adhesion, apoptosis and MAPK signaling pathway, were significantly enriched in both human and mouse gene sets (p < 0.05) (Fig 3A). The enrichment of VEGF signaling pathway, renin-angiotensin system, Toll-like receptor signaling pathway and GnRH signaling pathway was unique to the human gene set, whereas TGF-beta signaling pathway, p53 signaling pathway, Wnt signaling pathway, Hedgehog signaling pathway and cell cycle was enriched only in the mouse gene set (Fig 3A). Based on enrichment p-values, the most highly overrepresented pathway went to the LIF-STAT pathway. In this pathway, we identified 18 genes, of which 6 are specific to humans, 4 are specific to mice, and 8 are shared by both (Fig 3B). The LIF-STAT pathway is known to play an important role during decidualization in both humans [31] and mice [32–34].

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