sscMap：一个可扩展的Java应用程序，用于使用基因表达签名连接小分子药物
sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures
摘要：
背景资料：连接性图谱是通过将小分子的基因表达特征与数据库中的其他特征进行比较来识别小分子中的新药理学和毒理学性质的过程。最近开发了一种简单而稳健的方法，用于具有增加的特异性和灵敏度的连接性映射，并且使用实验获得的基因签名证明了其效用。结果如下：本文介绍了sscMap（statistically significant connections' map），这是一个Java应用程序，旨在使用最近发布的方法执行连接映射任务。该软件与默认的参考基因表达图谱集合捆绑在一起，该参考图谱基于Broad Institute Connectivity Map 02的公开数据集，其中包括来自7000多个Affymbre微阵列的数据，用于1000多个小分子化合物，以及5个人类细胞系中的6100个治疗实例。此外，该应用程序允许用户添加他们的参考配置文件的自定义集合，并适用于广泛的其他组学技术。结论：sscMap的效用是双重的。首先，它用于在用户提供的基因签名和基于布罗德研究所扩展数据集的6100个核心参考谱之间建立统计学显著联系。第二，它允许用户将同样的改进方法应用于定制的参考概况，这些概况可以添加到数据库中供将来参考。该软件可以从http://purl.oclc.org/NET/sscMap免费下载
英文摘要：
Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. Results: This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. Conclusions: The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
