Network analysis reveals important genes in human placenta

Aim To determine which genes are important in placenta by network analysis. Methods Placenta expressing genes were screened from RNA‐Seq data. Protein–protein interaction data were downloaded from STRING (v11.0) database. Google PageRank (PR) algorithm was used to identify important placental genes...

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Bibliographic Details
Published in:The journal of obstetrics and gynaecology research 2021-08, Vol.47 (8), p.2607-2615
Main Authors: Lin, Peihong, Lai, Xuedan, Wu, Ling, Liu, Wei, Lin, Shiqiang, Ye, Jianwen
Format: Article
Language:English
Subjects:
Actins - genetics
cytotrophoblast
extravillous trophoblast
Female
fetal growth restriction
Fetuses
gestational diabetes mellitus
Glyceraldehyde-3-phosphate dehydrogenase
Humans
Infant, Newborn
Placenta
Placenta Diseases
Pre-eclampsia
Pre-Eclampsia - genetics
Preeclampsia
Pregnancy
Premature Birth
preterm birth
Proteins
Superoxide dismutase
Superoxide Dismutase-1 - genetics
syncytiotrophoblast
TLR4 protein
Toll-like receptors
transcriptome
Trophoblasts
Ubiquitin - genetics
Ubiquitin-Protein Ligases - genetics
villous stromal cell
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Summary:Aim To determine which genes are important in placenta by network analysis. Methods Placenta expressing genes were screened from RNA‐Seq data. Protein–protein interaction data were downloaded from STRING (v11.0) database. Google PageRank (PR) algorithm was used to identify important placental genes from protein interaction network. Six placental disease‐related datasets were downloaded from NCBI GEO database, and the differential expression of the 99 genes was identified. Results We calculated PR for each placenta expressing gene and defined the top 99 genes with high PR as important genes. GAPDH has the highest PR. The 99 genes had different expression pattern in placental cell types. FN1 is up‐regulated in 8 w EVT compared to 8 w CTB and 24 w EVT compared to 8 w EVT. HSPA4 is down‐regulated in 8 w EVT compared to 8 w CTB and 24 w EVT compared to 8 w EVT. MIB2, TLR4, and UBB are consistently changed in preeclampsia (PE). UBB and ACTG1 were identified to be down‐regulated in fetal growth restriction (FGR). SOD1 is down‐regulated in preterm birth placenta. Conclusion Our findings confirmed that the importance of these genes in placenta‐related diseases, and provide new candidates (MIB2, UBB, ACTG1, and SOD1) for placenta‐related disease diagnosis and treatment.
ISSN:1341-8076
1447-0756
DOI:10.1111/jog.14820