Department of Microbial and Molecular Systems, Katholieke Universiteit Leuven, Heverlee-Leuven, Belgium.
PLoS One. 2011;6(7):e20938. doi: 10.1371/journal.pone.0020938. Epub 2011 Jul 14.
Microarrays are the main technology for large-scale transcriptional gene expression profiling, but the large bodies of data available in public databases are not useful due to the large heterogeneity. There are several initiatives that attempt to bundle these data into expression compendia, but such resources for bacterial organisms are scarce and limited to integration of experiments from the same platform or to indirect integration of per experiment analysis results.
METHODOLOGY/PRINCIPAL FINDINGS: We have constructed comprehensive organism-specific cross-platform expression compendia for three bacterial model organisms (Escherichia coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium) together with an access portal, dubbed COLOMBOS, that not only provides easy access to the compendia, but also includes a suite of tools for exploring, analyzing, and visualizing the data within these compendia. It is freely available at http://bioi.biw.kuleuven.be/colombos. The compendia are unique in directly combining expression information from different microarray platforms and experiments, and we illustrate the potential benefits of this direct integration with a case study: extending the known regulon of the Fur transcription factor of E. coli. The compendia also incorporate extensive annotations for both genes and experimental conditions; these heterogeneous data are functionally integrated in the COLOMBOS analysis tools to interactively browse and query the compendia not only for specific genes or experiments, but also metabolic pathways, transcriptional regulation mechanisms, experimental conditions, biological processes, etc.
CONCLUSIONS/SIGNIFICANCE: We have created cross-platform expression compendia for several bacterial organisms and developed a complementary access port COLOMBOS, that also serves as a convenient expression analysis tool to extract useful biological information. This work is relevant to a large community of microbiologists by facilitating the use of publicly available microarray experiments to support their research.
微阵列是大规模转录基因表达谱分析的主要技术，但由于存在较大的异质性，公共数据库中提供的大量数据没有用处。有几个计划试图将这些数据捆绑到表达总库中，但对于细菌生物体的此类资源很少，并且仅限于整合来自同一平台的实验，或者间接整合每个实验的分析结果。
方法/主要发现：我们为三种细菌模式生物（大肠杆菌、枯草芽孢杆菌和鼠伤寒沙门氏菌）构建了综合的特定于生物体的跨平台表达总库，以及一个名为 COLOMBOS 的访问门户，该门户不仅提供了对总库的轻松访问，还包括了一套用于探索、分析和可视化总库中数据的工具。它可免费在 http://bioi.biw.kuleuven.be/colombos 获得。这些总库的独特之处在于直接组合来自不同微阵列平台和实验的表达信息，我们通过一个案例研究来说明这种直接集成的潜在好处：扩展大肠杆菌 Fur 转录因子的已知调控子。这些总库还包含了基因和实验条件的广泛注释；这些异构数据在 COLOMBOS 分析工具中以功能方式集成，以便不仅可以针对特定基因或实验，还可以针对代谢途径、转录调控机制、实验条件、生物过程等进行交互式浏览和查询总库。
结论/意义：我们为几种细菌生物体创建了跨平台表达总库，并开发了一个补充的访问门户 COLOMBOS，该门户还可用作方便的表达分析工具，以提取有用的生物学信息。这项工作通过促进对公开可用的微阵列实验的使用，为广大微生物学家提供了便利，从而具有相关性。
