Gene expression profiling of cells, tissues, and developmental stages of the nematode C-elegans
Gene expression profiling of cells, tissues, and developmental stages of the nematode C-elegans
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DOI：
10.1101/sqb.2003.68.159
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发表时间：
2003-01-01
期刊：
影响因子：
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通讯作者：
Moerman, DG
中科院分区：
文献类型：
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作者：
McKay, SJ;Johnsen, R;Moerman, DG
我们的研究重点是线虫与人类基因的同源性。与INPARANOID （Remm et al. 2001）的两种预测蛋白质组比较，鉴定出4367种秀丽隐杆线虫蛋白质可能与人类同源（http://inparanoid）。cgb。吻。se)。这个基因列表提供了一个极好的机会，利用蠕虫来推断可能与人类生物学和卫生保健相关的基因的生物学信息。特别感兴趣的是预测的蠕虫/人类同源物，但没有关于功能的数据；超过一半的蠕虫同源词没有与之相关的功能注释。这些是特别重要的基因目标，因为它们可能形成一组新的“罗塞塔石碑”蛋白质。在我们的目标基因列表选择中使用的大部分基因组注释来自于WormBase （www.wormbase）。wormbase。组织;Stein et al. 2001；Harris et al. 2003)。筛选列表以去除与操纵子相关的rRNA基因和SL2反式剪接受体位点的基因（Blumenthal 1995; Blumenthal et al. 2002）。同样被移除的还有带有特征mrna的基因，这表明该基因已经得到了很好的研究。优先选择est确认的5个末端和胚胎期在Intronerator中表达的基因（Kent and Zahler 2000）。我们没有移除其他研究人员构建报告基因融合的基因，因为这些基因作为我们工作的控制集。事实上，到目前为止，我们观察到的启动子：：GFP结构的表达模式至少有四个例子与其他研究者使用抗体或功能性GFP融合物观察到的表达模式相同。
Our study focuses on nematode homologs of human genes. A comparison of the two predicted proteomes with INPARANOID (Remm et al. 2001) identified 4367 C. elegans proteins with probable human orthologs (http://inparanoid. cgb. ki. se). This list of genes provides an excellent opportunity to use the worm to infer biological information for genes potentially relevant to human biology and health care. Of particular interest are predicted worm/human homologs for which there are no data concerning function; more than half of the worm orthologs have no functional annotation associated with them. These are particularly important gene targets, as they may form a new set of “Rosetta stone” proteins.Most of the genome annotations used in the selection of our list of target genes were obtained from WormBase (www. wormbase. org; Stein et al. 2001; Harris et al. 2003). The list was filtered to remove rRNA genes and genes with SL2 trans-splice acceptor sites, which are associated with operons (Blumenthal 1995; Blumenthal et al. 2002). Also removed were genes with characterized mRNAs, an indication that the gene was already well studied. Preference was given to genes with EST-confirmed 5 ends and those identified as embryonically expressed in Intronerator (Kent and Zahler 2000). We did not remove genes for which other researchers have constructed reporter fusions, because such genes act as a control set for our work. Indeed, thus far, at least four examples of expression patterns we have observed with our promoter:: GFP constructs are identical to those observed by other investigators using either antibodies or functional GFP fusions.