基于芯片数据和整合分析研究奶牛乳房炎的关键通路

doi:10.16431/j.cnki.1671-7236.2016.04.003

›› 2016, Vol. 43 ›› Issue (4): 862-869.doi: 10.16431/j.cnki.1671-7236.2016.04.003

基于芯片数据和整合分析研究奶牛乳房炎的关键通路

赵静^1,2, 陈振亮^1,2, 王振^1,2, 张哲^1,2, 肖倩^1,2, 管毓渝^1,2, 孙浩^1,2, 刘光磊^3,4, 张向喆^1,2, 潘玉春^1,2, 廖荣荣^1,5, 王起山^1,2

1. 上海交通大学农业与生物学院, 上海 200240;
2. 上海市兽医生物技术重点实验室, 上海 200240;
3. 上海光明荷斯坦牧业有限公司, 上海 200246;
4. 上海奶牛育种中心股份有限公司, 上海 200246;
5. 上海市农业科学院畜牧所, 上海 200246

收稿日期:2015-09-21 出版日期:2016-04-20 发布日期:2016-04-27
通讯作者: 王起山 E-mail:wangqishan@sjtu.edu.cn
作者简介:赵静(1990-),女,河北石家庄人,硕士生,研究方向:统计基因组学与生物信息学,E-mail:zhaojingZJ@sjtu.edu.cn
基金资助:
上海市农委科技兴农攻关项目——基因组高密度SNP分子标记技术开发利用(沪农科攻字(2012)第2-3号)和南方大城市奶牛健康养殖生产技术集成及产业化示范(2012BAD12B08)

Study on the Critical Pathways of Dairy Cow Mastitis Based on Microarray Dataset and Integration Analysis

ZHAO Jing^1,2, CHEN Zhen-liang^1,2, WANG Zhen^1,2, ZHANG Zhe^1,2, XIAO Qian^1,2, GUAN Yu-yu^1,2, SUN Hao^1,2, LIU Guang-lei^3,4, ZHANG Xiang-zhe^1,2, PAN Yu-chun^1,2, LIAO Rong-rong^1,5, WANG Qi-shan^1,2

1. School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China;
2. Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, China;
3. Shanghai Bright Holstein Co., Ltd., Shanghai 200246, China;
4. Shanghai Dairy Cattle Breeding Center Co., Ltd., Shanghai 200246, China;
5. Animal Husbandry and Veterinanry Institute, Shanghai Academy of Agricultural Sciences, Shanghai 200246, China

Received:2015-09-21 Online:2016-04-20 Published:2016-04-27

摘要/Abstract

摘要： 奶牛乳房炎是奶牛的常见病和多发病之一,给奶牛业带来巨大的经济损失,严重制约着奶牛业的发展。为了进一步了解乳房炎的调控机理,对已发表的5套大肠杆菌感染奶牛乳腺上皮细胞的表达谱芯片数据统一进行预处理,并整合大肠杆菌感染1、6、24 h的基因富集分析,以期得到更可靠的影响奶牛乳房炎的关键基因和通路。结果发现,感染1、6和24 h数据集的分析结果中共同下调通路分别为9、30和17个,分析结果确定了一些奶牛乳房炎相关的通路及基因,为进一步揭示其调控机理提供参考。

关键词: 奶牛; 乳房炎; 基因富集分析; 通路

Abstract: Dairy cow mastitis was one of the common diseases and frequently-occurring diseases, caused huge economic losses, and also severely restricted the development of dairy industry.To further understand the regulation mechanism of mastitis, published five sets of related microarray data sets of cow mammary epithelial cells infected by Escherichia coli were collected, preprocessed with the standardized method, and integrat the result of gene set enrichment analysis with the infection time of 1, 6 and 24 h, so as to get more reliable key genes and pathways which could affect dairy cow mastitis.We find 9 down-regulated pathways common in the infected 1 h data sets, 30 down-regulated pathways common in the infected 6 h data sets, 17 down-regulated pathways common in the infected 24 h data sets.After analysis, we identified a number of dairy cow mastitis related pathways and genes, which would provide a reference for further study of regulation mechanisms.

Key words: dairy cow; mastitis; gene set enrichment analysis; pathway

中图分类号:

S857.2⁺6

赵静, 陈振亮, 王振, 张哲, 肖倩, 管毓渝, 孙浩, 刘光磊, 张向喆, 潘玉春, 廖荣荣, 王起山. 基于芯片数据和整合分析研究奶牛乳房炎的关键通路[J]. , 2016, 43(4): 862-869.

ZHAO Jing, CHEN Zhen-liang, WANG Zhen, ZHANG Zhe, XIAO Qian, GUAN Yu-yu, SUN Hao, LIU Guang-lei, ZHANG Xiang-zhe, PAN Yu-chun, LIAO Rong-rong, WANG Qi-shan. Study on the Critical Pathways of Dairy Cow Mastitis Based on Microarray Dataset and Integration Analysis[J]. , 2016, 43(4): 862-869.

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基于芯片数据和整合分析研究奶牛乳房炎的关键通路

Study on the Critical Pathways of Dairy Cow Mastitis Based on Microarray Dataset and Integration Analysis

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