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Serial gene co-expression network approach to mine biological meanings from integrated transcriptomes of the porcine endometrium during estrous cycle

Authors
Srikanth, KrishnamoorthyPark, WonCheoulLim, DajeongLee, Kyung TaiJang, Gul WonChoi, Bong HwanKa, HakhyunPark, Jong-EunKim, Jun-Mo
Issue Date
Jan-2020
Publisher
Springer Verlag
Keywords
DEGs; Estrous cycle; Gene co-expression network; Porcine endometrium; RNA-seq
Citation
Functional and Integrative Genomics, v.20, no.1, pp 117 - 131
Pages
15
Journal Title
Functional and Integrative Genomics
Volume
20
Number
1
Start Page
117
End Page
131
URI
https://scholarworks.bwise.kr/cau/handle/2019.sw.cau/36464
DOI
10.1007/s10142-019-00703-1
ISSN
1438-793X
1438-7948
Abstract
The estrous cycle is a complex process regulated by several hormones. To understand the dynamic changes in gene expression that takes place in the swine endometrium during the estrous cycle relative to the day of estrus onset, we performed RNA-sequencing analysis on days 0, 3, 6, 9, 12, 15, and 18, resulting in the identification of 4495 differentially expressed genes (DEGs; Q ≤ 0.05 and |log2FC| ≥ 1) at various phases in the estrous cycle. These DEGs were integrated into multiple gene co-expression networks based on different fold changes and correlation coefficient (R2) thresholds and a suitable network, which included 899 genes (|log2FC| ≥ 2 and R2 ≥ 0.99), was identified for downstream analyses based on the biological relevance of the Gene Ontology (GO) terms enriched. The genes in this network were partitioned into 6 clusters based on the expression pattern. Several GO terms including cell cycle, apoptosis, hormone signaling, and lipid biosynthetic process were found to be enriched. Furthermore, we found 15 significant KEGG pathways, including cell adhesion molecules, cytokine-cytokine receptor signaling, steroid biosynthesis, and estrogen signaling pathways. We identified several genes and GO terms to be stage-specific. Moreover, the identified genes and pathways extend our understanding of porcine endometrial regulation during estrous cycle and will serve as a good resource for future studies. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.
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