ProfileDB: A resource for proteomics and cross-omics biomarker discovery
ProfileDB: A resource for proteomics and cross-omics biomarker discovery
复制标题
DOI：
10.1016/j.bbapap.2013.11.007
复制
发表时间：
2014-05-01
影响因子：
3.2
通讯作者：
Schuchhardt，Johannes
中科院分区：
文献类型：
--
作者：
Bauer，Chris;Glintschert，Alexander;Schuchhardt，Johannes
高通量数据集的规模和复杂性不断增加，给研究人员带来了越来越大的挑战。通常采用具有单独数据分析管道的非常不同的（交叉组学）技术，使得统一的生物标志物发现策略和不同实验的直接比较困难且耗时。在这里，我们提出了全面的基于Web的应用程序ProfileDB。该应用程序旨在将来自不同高通量“组学”数据类型（转录组学、蛋白质组学、代谢组学）的数据与临床参数以及有关途径和本体的先验知识相整合。除了数据存储，ProfileDB还提供了一套用于研究检查和数据可视化的专用工具。用户只需点击几下鼠标就可以深入了解复杂的实验。我们将通过展示用于识别蛋白质组学生物标志物的典型用例来展示该应用。所有呈现的分析都可以使用公共ProfileDB Web服务器复制。ProfileDB应用程序可通过标准浏览器（Firefox 18 +，Internet Explorer版本9 +）技术通过http：//profileDB获得。microdiscovery.de/（登录和口令：profileDB）。该装置包含几个公共数据集，包括不同的交叉“组学”实验。本文是题为：生物标志物：蛋白质组学挑战的特刊的一部分。
The increasing size and complexity of high-throughput datasets pose a growing challenge for researchers. Often very different (cross-omics) techniques with individual data analysis pipelines are employed making a unified biomarker discovery strategy and a direct comparison of different experiments difficult and time consuming. Here we present the comprehensive web-based application ProfileDB. The application is designed to integrate data from different high-throughput ‘omics’ data types (Transcriptomics, Proteomics, Metabolomics) with clinical parameters and prior knowledge on pathways and ontologies. Beyond data storage, ProfileDB provides a set of dedicated tools for study inspection and data visualization. The user can gain insights into a complex experiment with just a few mouse clicks. We will demonstrate the application by presenting typical use cases for the identification of proteomics biomarkers. All presented analyses can be reproduced using the public ProfileDB web server. The ProfileDB application is available by standard browser (Firefox 18 +, Internet Explorer Version 9 +) technology via http://profileDB.-microdiscovery.de/ (login and pass − word: profileDB). The installation contains several public datasets including different cross-‘omics’ experiments. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.