McCarroll Steven A, Murphy Coleen T, Zou Sige, Pletcher Scott D, Chin Chen-Shan, Jan Yuh Nung, Kenyon Cynthia, Bargmann Cornelia I, Li Hao
Program in Neuroscience, University of California, San Francisco, California 94143, USA.
Nat Genet. 2004 Feb;36(2):197-204. doi: 10.1038/ng1291. Epub 2004 Jan 18.
We developed a method for systematically comparing gene expression patterns across organisms using genome-wide comparative analysis of DNA microarray experiments. We identified analogous gene expression programs comprising shared patterns of regulation across orthologous genes. Biological features of these patterns could be identified as highly conserved subpatterns that correspond to Gene Ontology categories. Here, we demonstrate these methods by analyzing a specific biological process, aging, and show that similar analysis can be applied to a range of biological processes. We found that two highly diverged animals, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, implement a shared adult-onset expression program of genes involved in mitochondrial metabolism, DNA repair, catabolism, peptidolysis and cellular transport. Most of these changes were implemented early in adulthood. Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and mRNA degradation.
我们开发了一种方法，通过对DNA微阵列实验进行全基因组比较分析，系统地比较不同生物体之间的基因表达模式。我们识别出了类似的基因表达程序，这些程序包含直系同源基因间共享的调控模式。这些模式的生物学特征可被识别为与基因本体论类别相对应的高度保守的子模式。在这里，我们通过分析一个特定的生物学过程——衰老，来展示这些方法，并表明类似的分析可应用于一系列生物学过程。我们发现，两种高度分化的动物——线虫秀丽隐杆线虫和果蝇黑腹果蝇，实施了一个共享的成年期基因表达程序，该程序涉及线粒体代谢、DNA修复、分解代谢、肽分解和细胞运输。这些变化大多在成年早期发生。利用这种方法搜索基因表达数据数据库，我们在幼虫发育、胚胎发生、配子发生和mRNA降解过程中发现了保守的转录特征。
