MAPPI-DAT：用于来自高通量MAPPIT细胞微阵列平台的蛋白质-蛋白质相互作用数据的管理与分析

MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.

作者信息

Gupta Surya, De Puysseleyr Veronic, Van der Heyden José, Maddelein Davy, Lemmens Irma, Lievens Sam, Degroeve Sven, Tavernier Jan, Martens Lennart

机构信息

Medical Biotechnology Center, VIB, Ghent, Belgium.

Department of Biochemistry, Ghent University, Ghent, Belgium.

出版信息

Bioinformatics. 2017 May 1;33(9):1424-1425. doi: 10.1093/bioinformatics/btx014.

DOI:10.1093/bioinformatics/btx014

PMID:28453684

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5408788/

Abstract

SUMMARY

Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments.

AVAILABILITY AND IMPLEMENTATION

MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT.

CONTACT

jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

蛋白质-蛋白质相互作用（PPI）研究极大地扩展了我们对不同条件下细胞行为和发育的认识。为实现蛋白质组规模的PPI研究覆盖，已开发了多种高通量PPI技术，包括基于微阵列的哺乳动物蛋白质-蛋白质相互作用陷阱（MAPPIT）系统。由于此类高通量技术通常会报告数千种相互作用，管理和分析大量获取的数据是一项挑战。因此，我们构建了MAPPIT细胞微阵列蛋白质-蛋白质相互作用数据管理与分析工具（MAPPI-DAT），作为用于MAPPIT细胞微阵列实验的自动化数据管理和分析工具。MAPPI-DAT以系统且结构化的方式存储实验数据和元数据，自动进行数据分析和解读，并能对所有存储实验中的MAPPIT细胞微阵列数据进行荟萃分析。

可用性与实现方式

MAPPI-DAT用Python开发，使用R进行数据分析，以MySQL作为数据管理系统。MAPPI-DAT是跨平台的，可在Microsoft Windows、Linux和OS X/macOS上运行。源代码和Microsoft Windows可执行文件可在https://github.com/compomics/MAPPI-DAT上根据宽松的Apache2开源许可免费获取。