Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia.
Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia.
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DOI：
10.1186/1471-2164-14-518
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发表时间：
2013-07-30
期刊：
影响因子：
4.4
通讯作者：
Dow JA
中科院分区：
文献类型：
--
作者：
Chintapalli VR;Wang J;Herzyk P;Davies SA;Dow JA
组织特异性转录本的比较分析是揭示组织功能的一项强有力的技术。我们的FlyAtlas.org为果蝇的多个组织提供了权威的基因表达水平(1)。虽然这类资源的主要用途是单基因查找，但有可能用强大的荟萃分析来解决以其他方式无法轻易框定的问题。在这里，我们通过比较上皮转录来确定一组核心的高表达基因，在成虫和幼虫的四种主要上皮组织(唾液腺、马氏管、中肠和后肠)上展示了FlyAtlas数据挖掘的力量。采用平行假说引导和无假说的方法来确定支撑昆虫上皮功能的核心基因。在前者中，基因列表是根据文献中确定的运输过程创建的，其表达谱来自flyatlas.org在线数据集。在后者中，为每个上皮细胞准备了基因富集表，并确定了在运输上皮细胞中持续富含的基因(包括运输相关的和无关的)。与整个苍蝇相比，一组关键的运输基因，包括V-ATPase、阳离子交换器、水通道蛋白、钾和氯通道以及碳酸氢酶，被发现在上皮组织中高度丰富。此外，另一组没有被预测具有上皮作用的基因与核心转运蛋白共表达，扩展了我们对运输上皮起作用的观点。通过研究在每种上皮中唯一过度表达的基因，获得了进一步的见解；例如，唾液腺表达脂肪酶，中肠有机溶质转运体，专门用于嘌呤代谢的小管，以及后肠过度表达仍未知的基因。综上所述，这些数据为这种关键模式昆虫的上皮功能提供了独特的见解，并为与其他物种进行比较提供了一个框架。它们还为FlyAtlas.org和其他多组织表达数据集提供了一种以功能为导向的数据挖掘方法。
Comparative analysis of tissue-specific transcriptomes is a powerful technique to uncover tissue functions. Our FlyAtlas.org provides authoritative gene expression levels for multiple tissues of Drosophila melanogaster (1). Although the main use of such resources is single gene lookup, there is the potential for powerful meta-analysis to address questions that could not easily be framed otherwise. Here, we illustrate the power of data-mining of FlyAtlas data by comparing epithelial transcriptomes to identify a core set of highly-expressed genes, across the four major epithelial tissues (salivary glands, Malpighian tubules, midgut and hindgut) of both adults and larvae. Parallel hypothesis-led and hypothesis-free approaches were adopted to identify core genes that underpin insect epithelial function. In the former, gene lists were created from transport processes identified in the literature, and their expression profiles mapped from the flyatlas.org online dataset. In the latter, gene enrichment lists were prepared for each epithelium, and genes (both transport related and unrelated) consistently enriched in transporting epithelia identified. A key set of transport genes, comprising V-ATPases, cation exchangers, aquaporins, potassium and chloride channels, and carbonic anhydrase, was found to be highly enriched across the epithelial tissues, compared with the whole fly. Additionally, a further set of genes that had not been predicted to have epithelial roles, were co-expressed with the core transporters, extending our view of what makes a transporting epithelium work. Further insights were obtained by studying the genes uniquely overexpressed in each epithelium; for example, the salivary gland expresses lipases, the midgut organic solute transporters, the tubules specialize for purine metabolism and the hindgut overexpresses still unknown genes. Taken together, these data provide a unique insight into epithelial function in this key model insect, and a framework for comparison with other species. They also provide a methodology for function-led datamining of FlyAtlas.org and other multi-tissue expression datasets.
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