The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK.
BMC Biol. 2012 Nov 15;10:90. doi: 10.1186/1741-7007-10-90.
This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering.
The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development.
As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas.
本研究描述了猪转录组的全基因组分析。为了全面覆盖已知的猪转录组，我们设计了一种新型猪 Affymetrix 表达谱芯片。我们利用该芯片生成了源自 62 种组织/细胞类型的猪组织的全基因组表达图谱。对这些数据进行了网络相关分析和聚类。
本研究提供了猪转录组的详细功能聚类，根据表达模式对转录本进行分组，因此可以根据未知基因的相关基因和表达位置来推断其功能。我们描述了组织图谱中存在的总体转录特征，尽可能将这些特征分配到特定的细胞群或途径。特别是，我们讨论了与胃肠道相关的表达特征，该器官沿其长度的 15 个部位进行了采样，其生物学在猪和人类中相似。我们确定了一组定义特定细胞区室和区域特异性消化功能的基因。最后，我们对胃肠道中表达的转录因子进行了网络分析，并展示了它们如何细分为可能控制细胞胃肠道发育的功能组。
猪作为一种重要的家畜动物，其生理学与人类比与小鼠更相似，因此为我们提供了一个重要的新资源，用于了解与哺乳动物组织和细胞的已知生理学相关的基因表达。数据和分析可在以下网站上获得：http://biogps.org 和 http://www.macrophages.com/pig-atlas。
