Masseroli Marco, Martucci Dario, Pinciroli Francesco
Bioengineering Department, Politecnico di Milano, I-20133 Milano, Italy.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W293-300. doi: 10.1093/nar/gkh432.
Statistical and clustering analyses of gene expression results from high-density microarray experiments produce lists of hundreds of genes regulated differentially, or with particular expression profiles, in the conditions under study. Independent of the microarray platforms and analysis methods used, these lists must be biologically interpreted to gain a better knowledge of the patho-physiological phenomena involved. To this end, numerous biological annotations are available within heterogeneous and widely distributed databases. Although several tools have been developed for annotating lists of genes, most of them do not give methods for evaluating the relevance of the annotations provided, or for estimating the functional bias introduced by the gene set on the array used to identify the gene list considered. We developed Genome Functional INtegrated Discoverer (GFINDer), a web server able to automatically provide large-scale lists of user-classified genes with functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list and calculates statistical significance values for each category. Moreover, GFINDer enables the functional classification of genes according to mined functional categories and the statistical analysis is of the classifications obtained, aiding better interpretation of microarray experiment results. GFINDer is available online at http://www.medinfopoli.polimi.it/GFINDer/.
对来自高密度微阵列实验的基因表达结果进行统计和聚类分析，会生成在研究条件下差异调节或具有特定表达谱的数百个基因列表。无论使用何种微阵列平台和分析方法，都必须对这些列表进行生物学解释，以便更好地了解所涉及的病理生理现象。为此，在异构且分布广泛的数据库中可获得大量生物学注释。尽管已经开发了几种用于注释基因列表的工具，但其中大多数都没有提供评估所提供注释相关性的方法，也没有提供估计用于识别所考虑基因列表的阵列上的基因集所引入的功能偏差的方法。我们开发了基因组功能综合发现器（GFINDer），这是一个网络服务器，能够自动为用户分类的基因大规模列表提供功能概况，从生物学角度表征列表中不同基因类别。GFINDer会自动从不同来源检索多个功能类别的注释，识别用户分类基因列表中每个类别中富集的类别，并计算每个类别的统计显著性值。此外，GFINDer能够根据挖掘出的功能类别对基因进行功能分类，并对获得的分类进行统计分析，有助于更好地解释微阵列实验结果。可通过http://www.medinfopoli.polimi.it/GFINDer/在线访问GFINDer。
