Draghici Sorin, Khatri Purvesh, Shah Abhik, Tainsky Michael A
Department of Computer Science, Wayne State University, Detroit, MI, USA.
Biotechniques. 2003 Mar;Suppl:55-61.
Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis-driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Because focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the Gene Ontology Consortium nomenclature. We used this tool to compare several arrays focused on apoptosis, oncogenes, and tumor suppressors. We considered arrays from BD Biosciences Clontech, PerkinElmer, Sigma-Genosys, and SuperArray. We showed that among the oncogene arrays, the PerkinElmer MICROMAX oncogene microarray has a better representation of oncogenesis, protein phosphorylation, and negative control of cell proliferation. The comparison of the apoptosis arrays showed that most apoptosis-related biological processes are equally well represented on the arrays considered. However, functional categories such as immune response, cell-cell signaling, cell-surface receptor linked signal transduction, and interleukins are better represented on the Sigma-Genoys Panorama human apoptosis array. At the same time, processes such as cell cycle control, oncogenesis, and negative control of cell proliferation are better represented on the BD Biosciences Clontech Atlas Select human apoptosis array.
微阵列处于生物技术革命的核心地位，使研究人员能够同时筛选数以万计的基因。通常，它们被用于探索性研究以帮助形成假设。在大多数情况下，这个阶段之后是一个更具针对性、由假设驱动的阶段，在此阶段中某些特定的生物过程和途径被认为涉及其中。由于单个生物过程仍可能涉及数百个基因，微阵列仍然是首选方法，几家制造商提供的针对性阵列就证明了这一点。因为不同制造商的针对性阵列使用不同的基因集，每个阵列将在不同程度上代表任何给定的调控途径。我们认为，对现有阵列进行功能分析应该是阵列选择中使用的最重要标准。我们开发了Onto-Compare作为一个数据库，它可以基于基因本体联合会的命名法提供此功能。我们使用这个工具比较了几种针对细胞凋亡、癌基因和肿瘤抑制基因的阵列。我们考虑了BD Biosciences Clontech、PerkinElmer、Sigma-Genosys和SuperArray的阵列。我们表明，在癌基因阵列中，PerkinElmer MICROMAX癌基因微阵列在肿瘤发生、蛋白质磷酸化和细胞增殖的负调控方面有更好的表现。细胞凋亡阵列的比较表明，大多数与细胞凋亡相关的生物过程在所考虑的阵列上表现得同样好。然而，免疫反应、细胞间信号传导、细胞表面受体连接的信号转导和白细胞介素等功能类别在Sigma-Genoys全景人类细胞凋亡阵列上表现得更好。同时，细胞周期控制、肿瘤发生和细胞增殖的负调控等过程在BD Biosciences Clontech Atlas Select人类细胞凋亡阵列上表现得更好。
