Center for Research in Molecular Genetics Fondazione CARISBO, Department of Histology, Embryology and Applied Biology, University of Bologna - Via Belmeloro, 8 - 40126 - Bologna, Italy.
BMC Genomics. 2011 Feb 18;12:121. doi: 10.1186/1471-2164-12-121.
Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input.
TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified.
TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes.
已经开发了几种工具来进行全局基因表达谱数据分析，以搜索特定的染色体区域，这些区域的特征符合定义的标准，并研究相邻基因的表达。然而，这些工具大多数都针对特定的用途和特定的上下文（例如，它们是特定于物种的，或者仅限于特定的数据格式），并且通常只接受基因列表作为输入。
TRAM（转录组映射器）是一种新的通用工具，它允许从任何源列表中生成和分析定量转录组图谱，这些源列表为给定的基因集提供基因表达值（例如表达微阵列），实现为关系数据库。它包括一个解析器，能够将基因标识符分配给来自不同数据源的唯一和更新的基因符号。此外，TRAM能够执行样本内和样本间的数据标准化，包括一种原始的分位数标准化（比例分位数）变体，可用于标准化来自具有高度不同数量研究基因的平台的数据。当处于“映射”模式时，该软件会生成样本（或样本池）的转录组的定量表示，并确定指定长度的片段是否相对于所需阈值过度/低表达。当处于“聚类”模式时，该软件会搜索一组过度/低表达的连续基因。所有结果的统计显著性都是相对于位于同一染色体上的基因或整个基因组基因计算的。可以轻松生成显示两个样本组之间差异表达的转录组图谱，相对于两种不同的生物条件。我们展示了基于人类 CD34+造血祖细胞样本池和巨核细胞样本池的元分析比较的生物学模型测试的结果。确定了在向巨核细胞分化过程中差异表达的生物学相关染色体片段和基因簇。
TRAM 旨在根据来自多个来源的基因表达数据创建和统计分析定量转录组图谱。该版本包括 FileMaker Pro 数据库管理运行时应用程序，并可在 http://apollo11.isto.unibo.it/software/ 上免费获得，同时还提供了人类、小鼠和斑马鱼转录组映射的预配置实现。
