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一个使用 shiny 来识别最相似突变特征的网络应用程序。

: a web application to identify the most similar mutational signature using shiny.

机构信息

Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, 2001 N.Soto Street, Los Angeles, CA, 91003, USA.

出版信息

F1000Res. 2020 Jun 10;9:586. doi: 10.12688/f1000research.24435.2. eCollection 2020.

Abstract

There are two frameworks for characterizing mutational signatures which are commonly used to describe the nucleotide patterns that arise from mutational processes. Estimated mutational signatures from fitting these two methods in human cancer can be found online, in the Catalogue Of Somatic Mutations In Cancer (COSMIC) website or a GitHub repository. The two frameworks make differing assumptions regarding independence of base pairs and for that reason may produce different results. Consequently, there is a need to compare and contrast the results of the two methods, but no such tool currently exists. In this paper, we provide a simple and intuitive interface that allows comparisons of pairs of mutational signatures to be easily performed. Cosine similarity measures the extent of signature similarity. To compare mutational signatures of different formats, one signature type (COSMIC or ) is converted to the format of the other before the signatures are compared. provides a simple and user-friendly web application allowing researchers to download published mutational signatures of either type and to compare signatures from COSMIC to those from , and vice versa. Furthermore, allows users to input a self-defined mutational signature and examine its similarity to published signatures from both data sources. is accessible online and source code is available for download from GitHub.

摘要

有两种用于描述突变过程中产生的核苷酸模式的突变特征描述框架,常用于医学专业学术文献的翻译。可以在在线的 Catalogue Of Somatic Mutations In Cancer (COSMIC) 网站或 GitHub 存储库中找到拟合这两种方法在人类癌症中得出的估计突变特征。这两个框架对碱基对的独立性有不同的假设,因此可能会产生不同的结果。因此,有必要比较和对比这两种方法的结果,但目前没有这样的工具。在本文中,我们提供了一个简单直观的界面,允许轻松地对突变特征对进行比较。余弦相似度衡量特征相似性的程度。为了比较不同格式的突变特征,在比较特征之前,将一种特征类型(COSMIC 或 )转换为另一种类型。 提供了一个简单易用的 Web 应用程序,允许研究人员下载这两种类型的已发布突变特征,并将 COSMIC 的特征与 的特征进行比较,反之亦然。此外, 允许用户输入自定义的突变特征,并检查其与来自两个数据源的已发布特征的相似性。 可在线访问,其源代码可从 GitHub 下载。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8661/7702169/03adf8698567/f1000research-9-30641-g0003.jpg

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