Bioinformatics Laboratory, Department of Experimental Medicine and Clinic, Magna Graecia University, Catanzaro, Italy.
BMC Bioinformatics. 2010 Jun 10;11:315. doi: 10.1186/1471-2105-11-315.
A main goal in understanding cell mechanisms is to explain the relationship among genes and related molecular processes through the combined use of technological platforms and bioinformatics analysis. High throughput platforms, such as microarrays, enable the investigation of the whole genome in a single experiment. There exist different kind of microarray platforms, that produce different types of binary data (images and raw data). Moreover, also considering a single vendor, different chips are available. The analysis of microarray data requires an initial preprocessing phase (i.e. normalization and summarization) of raw data that makes them suitable for use on existing platforms, such as the TIGR M4 Suite. Nevertheless, the annotations of data with additional information such as gene function, is needed to perform more powerful analysis. Raw data preprocessing and annotation is often performed in a manual and error prone way. Moreover, many available preprocessing tools do not support annotation. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of microarray data are needed.
The paper presents mu-CS (Microarray Cel file Summarizer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix binary data. mu-CS is based on a client-server architecture. The mu-CS client is provided both as a plug-in of the TIGR M4 platform and as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data, avoiding the manual invocation of external tools (e.g. the Affymetrix Power Tools), the manual loading of preprocessing libraries, and the management of intermediate files. The mu-CS server automatically updates the references to the summarization and annotation libraries that are provided to the mu-CS client before the preprocessing. The mu-CS server is based on the web services technology and can be easily extended to support more microarray vendors (e.g. Illumina).
Thus mu-CS users can directly manage binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the mu-CS plugin for TM4 can manage Affymetrix binary files without using external tools, such as APT (Affymetrix Power Tools) and related libraries. Consequently, mu-CS offers four main advantages: (i) it avoids to waste time for searching the correct libraries, (ii) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or the use of old libraries, (iii) it implements the annotation of preprocessed data, and finally, (iv) it may enhance the quality of further analysis since it provides the most updated annotation libraries. The mu-CS client is freely available as a plugin of the TM4 platform as well as a standalone application at the project web site (http://bioingegneria.unicz.it/M-CS).
理解细胞机制的主要目标是通过结合使用技术平台和生物信息学分析来解释基因与相关分子过程之间的关系。高通量平台，如微阵列，能够在单个实验中研究整个基因组。存在不同类型的微阵列平台，它们产生不同类型的二进制数据（图像和原始数据）。此外，即使考虑到单个供应商，也有不同的芯片可供选择。微阵列数据的分析需要对原始数据进行初始预处理（即标准化和汇总），使其适用于现有平台，如 TIGR M4 套件。然而，需要对数据进行额外信息（如基因功能）的注释，以便进行更强大的分析。原始数据的预处理和注释通常是手动进行的，并且容易出错。此外，许多可用的预处理工具不支持注释。因此，需要新的、与平台无关的、可能是开源的工具来实现微阵列数据的半自动预处理和注释。
本文介绍了 mu-CS（微阵列 Cel 文件汇总器），这是一种用于自动归一化、汇总和注释 Affymetrix 二进制数据的跨平台工具。mu-CS 基于客户端-服务器架构。mu-CS 客户端既作为 TIGR M4 平台的插件提供，也作为 Java 独立工具提供，使用户能够读取、预处理和分析二进制微阵列数据，避免手动调用外部工具（例如 Affymetrix Power Tools）、手动加载预处理库以及管理中间文件。mu-CS 服务器在预处理之前自动更新提供给 mu-CS 客户端的汇总和注释库的引用。mu-CS 服务器基于 Web 服务技术，可以轻松扩展以支持更多的微阵列供应商（例如 Illumina）。
因此，mu-CS 用户可以直接管理二进制数据，而不必担心查找和调用适当的预处理工具和芯片特定库。此外，使用 TM4 的 mu-CS 插件的用户可以在不使用外部工具（如 APT（Affymetrix Power Tools）和相关库）的情况下管理 Affymetrix 二进制文件。因此，mu-CS 提供了四个主要优势：（i）它避免了浪费时间搜索正确的库，（ii）它减少了预处理和进一步分析阶段可能出现的错误，例如由于参数选择不正确或使用旧库，（iii）它实现了预处理数据的注释，最后，（iv）它可能会提高进一步分析的质量，因为它提供了最新的注释库。mu-CS 客户端可作为 TM4 平台的插件以及项目网站（http://bioingegneria.unicz.it/M-CS）上的独立应用程序免费获得。
