SurfaceGenie：一个基于网络的应用程序，用于优先考虑细胞类型特异性标记候选物。
SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates.
机构信息
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
出版信息
Bioinformatics. 2020 Jun 1;36(11):3447-3456. doi: 10.1093/bioinformatics/btaa092.
MOTIVATION
Cell-type-specific surface proteins can be exploited as valuable markers for a range of applications including immunophenotyping live cells, targeted drug delivery and in vivo imaging. Despite their utility and relevance, the unique combination of molecules present at the cell surface are not yet described for most cell types. A significant challenge in analyzing 'omic' discovery datasets is the selection of candidate markers that are most applicable for downstream applications.
RESULTS
Here, we developed GenieScore, a prioritization metric that integrates a consensus-based prediction of cell surface localization with user-input data to rank-order candidate cell-type-specific surface markers. In this report, we demonstrate the utility of GenieScore for analyzing human and rodent data from proteomic and transcriptomic experiments in the areas of cancer, stem cell and islet biology. We also demonstrate that permutations of GenieScore, termed IsoGenieScore and OmniGenieScore, can efficiently prioritize co-expressed and intracellular cell-type-specific markers, respectively.
AVAILABILITY AND IMPLEMENTATION
Calculation of GenieScores and lookup of SPC scores is made freely accessible via the SurfaceGenie web application: www.cellsurfer.net/surfacegenie.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
细胞类型特异性表面蛋白可作为有价值的标记物，用于多种应用，包括活细胞免疫表型分析、靶向药物递送和体内成像。尽管它们具有实用性和相关性，但大多数细胞类型的细胞表面存在的分子的独特组合尚未被描述。在分析“组学”发现数据集时，一个重大挑战是选择最适用于下游应用的候选标记物。
结果
在这里，我们开发了 GenieScore，这是一种优先级度量标准，它将基于共识的细胞表面定位预测与用户输入数据相结合，对候选细胞类型特异性表面标记物进行排序。在本报告中，我们展示了 GenieScore 在分析来自蛋白质组学和转录组学实验的人类和啮齿动物数据方面的应用，这些数据涉及癌症、干细胞和胰岛生物学领域。我们还证明了 GenieScore 的排列，称为 IsoGenieScore 和 OmniGenieScore，分别可以有效地优先考虑共表达和细胞内细胞类型特异性标记物。
可用性和实现
GenieScores 的计算和 SPC 分数的查询可通过 SurfaceGenie 网络应用程序免费获得：www.cellsurfer.net/surfacegenie。
联系人
补充信息
补充数据可在 Bioinformatics 在线获得。
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