From gene networks to gene function
From gene networks to gene function
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DOI：
10.1101/gr.1111403
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发表时间：
2003-12-01
期刊：
影响因子：
7
通讯作者：
Brama, A
中科院分区：
文献类型：
--
作者：
Schlitt, T;Palin, K;Brama, A
我们提出了一种新的方法来识别功能相关的基因的基础上比较的邻域基因网络。这种方法不依赖于基因序列或蛋白质结构同源性，它可以应用于任何生物和各种各样的实验数据集。预测的基因关系的特征取决于潜在的网络;它们关注的是生物过程而不是分子功能。我们使用的方法来分析来自全基因组染色质免疫沉淀实验，大规模的基因缺失研究，并从酵母酿酒酵母的转录因子的共识结合位点的基因组位置的基因网络。我们确定了159个基因之间的816个功能关系，并表明这些关系对应于蛋白质-蛋白质相互作用，在相同的蛋白质复合物中共现，和/或在科学文章摘要中共现。我们的研究结果表明，7个以前未表征的酵母基因的功能：KIN 3和YMR 269 W可能参与与细胞生长和/或维持相关的生物过程，而IES 6，YEL 008 W，YEL 033 W，YHL 029 C，YMR 010 W和YMR 031 W-A可能具有代谢功能。
We propose a novel method to identify functionally related genes based on comparisons of neighborhoods in gene networks. This method does not rely on gene sequence or protein structure homologies, and it can be applied to any organism and a wide variety of experimental data sets. The character of the predicted gene relationships depends on the underlying networks; they concern biological processes rather than the molecular function. We used the method to analyze gene networks derived from genome-wide chromatin immunoprecipitation experiments, a large-scale gene deletion study, and from the genomic positions of consensus binding sites for transcription factors of the yeast Saccharomyces cerevisiae. We identified 816 functional relationships between 159 genes and show that these relationships correspond to protein-protein interactions, co-occurrence in the same protein complexes, and/or co-occurrence in abstracts of scientific articles. Our results suggest functions for seven previously uncharacterized yeast genes: KIN3 and YMR269W may be involved in biological processes related to cell growth and/or maintenance, whereas IES6, YEL008W, YEL033W, YHL029C, YMR010W, and YMR031W-A are likely to have metabolic functions.