Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
PLoS One. 2012;7(8):e43305. doi: 10.1371/journal.pone.0043305. Epub 2012 Aug 31.
The vast array of in silico resources and data of high throughput profiling currently available in life sciences research offer the possibility of aiding cancer gene and drug discovery process. Here we propose to take advantage of these resources to develop a tool, TARGETgene, for efficiently identifying mutation drivers, possible therapeutic targets, and drug candidates in cancer. The simple graphical user interface enables rapid, intuitive mapping and analysis at the systems level. Users can find, select, and explore identified target genes and compounds of interest (e.g., novel cancer genes and their enriched biological processes), and validate predictions using user-defined benchmark genes (e.g., target genes detected in RNAi screens) and curated cancer genes via TARGETgene. The high-level capabilities of TARGETgene are also demonstrated through two applications in this paper. The predictions in these two applications were then satisfactorily validated by several ways, including known cancer genes, results of RNAi screens, gene function annotations, and target genes of drugs that have been used or in clinical trial in cancer treatments. TARGETgene is freely available from the Biomedical Simulations Resource web site (http://bmsr.usc.edu/Software/TARGET/TARGET.html).
目前生命科学研究中存在大量的计算机资源和高通量分析数据，这为癌症基因和药物发现过程提供了帮助。在这里，我们建议利用这些资源开发一种工具 TARGETgene，以有效地识别癌症中的突变驱动基因、潜在治疗靶点和药物候选物。简单的图形用户界面支持快速直观的系统级映射和分析。用户可以找到、选择和探索感兴趣的目标基因和化合物（例如，新的癌症基因及其丰富的生物学过程），并使用用户定义的基准基因（例如，在 RNAi 筛选中检测到的靶基因）和经过精心整理的癌症基因通过 TARGETgene 来验证预测。本文中的两个应用程序也展示了 TARGETgene 的高级功能。通过多种方式，包括已知的癌症基因、RNAi 筛选结果、基因功能注释以及已用于癌症治疗或临床试验的药物的靶基因，对这两个应用程序中的预测进行了令人满意的验证。TARGETgene 可从生物医学模拟资源网站（http://bmsr.usc.edu/Software/TARGET/TARGET.html）免费获得。
