title: Data mining in networks of differentially expressed genes during sow pregnancy.
abstract: Small to moderate gains in Pig fertility can mean large returns in overall efficiency, and developing methods to improve it is highly desirable. High fertility rates depend on completion of successful pregnancies. To understand the molecular signals associated with pregnancy in sows, expression profiling experiments were conducted to identify differentially expressed genes in ovary and myometrium at different pregnancy periods using the Affymetrix Porcine GeneChip(TM). A total of 974, 1800, 335 and 710 differentially expressed transcripts were identified in the myometrium during early pregnancy (EP) and late pregnancy (LP), and in the ovary during EP and LP, respectively. Self-Organizing Map (SOM) clusters indicated the differentially expressed genes belonged to 7 different functional groups. Based on BLASTX searches and Gene Ontology (GO) classifications, 129 unique genes closely related to pregnancy showed differential expression patterns. GO analysis also indicated that there were 21 different molecular function categories, 20 different biological process categories, and 8 different cellular component categories of genes differentially expressed during sow pregnancy. Gene regulatory network reconstruction provided us with an interaction model of known genes such as insulin-like growth factor 2 (IGF2) gene, estrogen receptor (ESR) gene, retinol-binding protein-4 (RBP4) gene, and several unknown candidate genes related to reproduction. Several pitch point genes were selected for association study with reproduction traits. For instance, DPPA5 g.363 T>C was found to associate with litter born weight at later parities in Beijing Black pigs significantly (p < 0.05). Overall, this study contributes to elucidating the mechanism underlying pregnancy processes, which maybe provide valuable information for pig reproduction improvement.
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193 Beijing, China.
authors.forename: Ligang
authors.initials: L
authors.lastname: Wang
authors.forename: Longchao
authors.initials: L
authors.lastname: Zhang
authors.forename: Yong
authors.initials: Y
authors.lastname: Li
authors.forename: Wen
authors.initials: W
authors.lastname: Li
authors.forename: Weizhen
authors.initials: W
authors.lastname: Luo
authors.forename: Duxue
authors.initials: D
authors.lastname: Cheng
authors.forename: Hua
authors.initials: H
authors.lastname: Yan
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Ma
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Xin
authors.initials: X
authors.lastname: Song
authors.forename: Jing
authors.initials: J
authors.lastname: Liang
authors.forename: Kebin
authors.initials: K
authors.lastname: Zhao
authors.forename: Lixian
authors.initials: L
authors.lastname: Wang
mesh_terms: D000818:Animals; D057225:Data Mining / Q000379:methods*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D009215:Myometrium / Q000378:metabolism; D010053:Ovary / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D013552:Swine