Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy
<p>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, expres...
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| Format: | Article |
| Language: | English |
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Ivyspring International Publisher
2012-01-01
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| Series: | International Journal of Biological Sciences |
| Online Access: | http://www.biolsci.org/v08p0548.htm |
| _version_ | 1819130707616727040 |
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| author | Ligang Wang, Longchao Zhang, Yong Li, Wen Li, Weizhen Luo, Duxue Cheng, Hua Yan, Xiaojun Ma, Xin Liu, Xin Song, Jing Liang, Kebin Zhao, Lixian Wang |
| author_facet | Ligang Wang, Longchao Zhang, Yong Li, Wen Li, Weizhen Luo, Duxue Cheng, Hua Yan, Xiaojun Ma, Xin Liu, Xin Song, Jing Liang, Kebin Zhao, Lixian Wang |
| author_sort | Ligang Wang, Longchao Zhang, Yong Li, Wen Li, Weizhen Luo, Duxue Cheng, Hua Yan, Xiaojun Ma, Xin Liu, Xin Song, Jing Liang, Kebin Zhao, Lixian Wang |
| collection | DOAJ |
| description | <p>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<sup>TM</sup>. 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 (<i>IGF2</i>) gene, estrogen receptor (<i>ESR</i>) gene, retinol-binding protein-4 (<i>RBP4</i>) gene, and several unknown candidate genes related to reproduction. Several pitch point genes were selected for association study with reproduction traits. For instance, <i>DPPA5</i> g.363 T>C was found to associate with litter born weight at later parities in Beijing Black pigs significantly (<i>p</i> < 0.05). Overall, this study contributes to elucidating the mechanism underlying pregnancy processes, which maybe provide valuable information for pig reproduction improvement.</p> |
| first_indexed | 2024-12-22T09:03:54Z |
| format | Article |
| id | doaj.art-44cfd350e29c4f169f379f9d159ed8e3 |
| institution | Directory Open Access Journal |
| issn | 1449-2288 |
| language | English |
| last_indexed | 2024-12-22T09:03:54Z |
| publishDate | 2012-01-01 |
| publisher | Ivyspring International Publisher |
| record_format | Article |
| series | International Journal of Biological Sciences |
| spelling | doaj.art-44cfd350e29c4f169f379f9d159ed8e32022-12-21T18:31:39ZengIvyspring International PublisherInternational Journal of Biological Sciences1449-22882012-01-0184548560Data Mining in Networks of Differentially Expressed Genes during Sow PregnancyLigang Wang, Longchao Zhang, Yong Li, Wen Li, Weizhen Luo, Duxue Cheng, Hua Yan, Xiaojun Ma, Xin Liu, Xin Song, Jing Liang, Kebin Zhao, Lixian Wang<p>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<sup>TM</sup>. 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 (<i>IGF2</i>) gene, estrogen receptor (<i>ESR</i>) gene, retinol-binding protein-4 (<i>RBP4</i>) gene, and several unknown candidate genes related to reproduction. Several pitch point genes were selected for association study with reproduction traits. For instance, <i>DPPA5</i> g.363 T>C was found to associate with litter born weight at later parities in Beijing Black pigs significantly (<i>p</i> < 0.05). Overall, this study contributes to elucidating the mechanism underlying pregnancy processes, which maybe provide valuable information for pig reproduction improvement.</p>http://www.biolsci.org/v08p0548.htm |
| spellingShingle | Ligang Wang, Longchao Zhang, Yong Li, Wen Li, Weizhen Luo, Duxue Cheng, Hua Yan, Xiaojun Ma, Xin Liu, Xin Song, Jing Liang, Kebin Zhao, Lixian Wang Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy International Journal of Biological Sciences |
| title | Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy |
| title_full | Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy |
| title_fullStr | Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy |
| title_full_unstemmed | Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy |
| title_short | Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy |
| title_sort | data mining in networks of differentially expressed genes during sow pregnancy |
| url | http://www.biolsci.org/v08p0548.htm |
| work_keys_str_mv | AT ligangwanglongchaozhangyongliwenliweizhenluoduxuechenghuayanxiaojunmaxinliuxinsongjingliangkebinzhaolixianwang datamininginnetworksofdifferentiallyexpressedgenesduringsowpregnancy |