Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
复制标题
DOI：
10.1093/bioinformatics/bti662
复制
发表时间：
2005-11-01
期刊：
影响因子：
5.8
通讯作者：
Spang, R
中科院分区：
文献类型：
--
作者：
Markowetz, F;Bloch, J;Spang, R
动机：细胞信号传导途径，这不是在转录水平上调节，不能直接推导出表达谱实验。当RNA干扰或基因敲除等外部干预起作用时，情况发生了变化。即使信号基因的表达没有改变，在下游基因的二次效应揭示了通路，并允许部分重建其topology.Results：我们引入了一种算法来推断非转录通路功能的基础上差异基因表达沉默检测。我们证明了我们的算法在模拟研究的控制设置的权力，并解释其实际用途的背景下，RNA干扰数据集调查在果蝇微生物的挑战。
Motivation: Cellular signaling pathways, which are not modulated on a transcriptional level, cannot be directly deduced from expression profiling experiments. The situation changes, when external interventions such as RNA interference or gene knock-outs come into play. Even if the expression of the signaling genes is not changed, secondary effects in downstream genes shed light on the pathway, and allow partial reconstruction of its topology.Results: We introduce an algorithm to infer non-transcriptional pathway features based on differential gene expression in silencing assays. We demonstrate the power of our algorithm in the controlled setting of simulation studies, and explain its practical use in the context of an RNA interference dataset investigating the response to microbial challenge in Drosophila melanogaster.