Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.
Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.
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DOI：
10.1074/mcp.o115.048777
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发表时间：
2015-11
期刊：
影响因子：
--
通讯作者：
Bessant C
中科院分区：
文献类型：
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作者：
Fan J;Saha S;Barker G;Heesom KJ;Ghali F;Jones AR;Matthews DA;Bessant C
随着最近RNA-seq技术的出现，蛋白质组学社区已经开始为多肽和蛋白质鉴定生成特定样本的蛋白质数据库，这种方法我们称为蛋白质组学通过转录组学(PIT)获得信息。这种方法已经获得了许多兴趣，特别是在研究非模式生物或特别动态蛋白质组的研究人员中，例如在发育生物学和寄主病原体研究中观察到的蛋白质组。PIT已被证明可以提高已知蛋白质的覆盖率，并揭示潜在的新基因产品。然而，由于所需数据分析的复杂性，许多小组在使用PIT时受到阻碍。这种分析必然需要复杂地集成来自至少两个不同社区的许多不同的软件工具，而且由于PIT具有一系列生物应用程序，单一的软件管道并不适合所有用例。为了克服这些问题，我们创建了GIO，这是一个软件系统，使用成熟的Galaxy平台，通过简单的Web界面向典型的实验室科学家提供坑分析。在GIO中，我们为四种常见用例提供了工作流程：对照参考蛋白质组进行标准搜索；无需参考基因组的PIT蛋白质识别；使用基因组指南的PIT蛋白质识别；以及PIT基因组注释。这些工作流包括可在Web界面内重新配置和重新安排的各个工具，以创建新的工作流来支持其他用例。
With the recent advent of RNA-seq technology the proteomics community has begun to generate sample-specific protein databases for peptide and protein identification, an approach we call proteomics informed by transcriptomics (PIT). This approach has gained a lot of interest, particularly among researchers who work with nonmodel organisms or with particularly dynamic proteomes such as those observed in developmental biology and host-pathogen studies. PIT has been shown to improve coverage of known proteins, and to reveal potential novel gene products. However, many groups are impeded in their use of PIT by the complexity of the required data analysis. Necessarily, this analysis requires complex integration of a number of different software tools from at least two different communities, and because PIT has a range of biological applications a single software pipeline is not suitable for all use cases. To overcome these problems, we have created GIO, a software system that uses the well-established Galaxy platform to make PIT analysis available to the typical bench scientist via a simple web interface. Within GIO we provide workflows for four common use cases: a standard search against a reference proteome; PIT protein identification without a reference genome; PIT protein identification using a genome guide; and PIT genome annotation. These workflows comprise individual tools that can be reconfigured and rearranged within the web interface to create new workflows to support additional use cases.