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Systems biology has gained a tremendous amount of interest in the last few years. This is partly due to the realization that traditional approaches focusing only on a few molecules at a time cannot describe the impact of aberrant or modulated molecular environments across a whole system.Furthermore, a hypothesis-driven study aims to prove or disprove its postulations, whereas a hypothesis-free systems approach can yield an unbiased and novel testable hypothesis as an end-result. This latter approach foregoes assumptions which predict how a biological system should react to an altered micro-environment within a cellular context, across a tissue or impacting on distant organs. Additionally, re-use of existing data by systematic data mining and re-stratification, one of the cornerstones of integrative systems biology, is also gaining attention. While tremendous efforts using a systems methodology have already yielded excellent results, it is apparent that a lack of suitable analytic tools and purpose-built databases poses a major bottleneck in applying a systematic work flow. This review addresses the current approaches used in systems analysis and obstacles often encountered in large-scale data analysis and integration which tend to go unnoticed, but have a direct impact on the final outcome of a systems approach. Its wide applicability, ranging from basic research, disease descriptors, pharmacological studies, to personalized medicine, makes this emerging approach well suited to address biological and medical questions where conventional methods are not ideal. 摘要 在过去几年里,系统生物学已经获得了人们极大的关注。部分原因是人们认识到传统方法在同一时间只能聚焦几个分子,无法对跨系统异常分子所产生的影响或调节的分子环境进行描述。此外,假设驱动研究旨在证明或反驳它的假定,然而假设无系统研究最终可以产生一个不带偏见的、新颖可检验的假设。第二种方法放弃了能预测生物系统在细胞内如何通过组织或对影响远处器官来应对变化了的微环境的所有假设。另外,挖掘系统数据和重新分类整理现存资料后重新使用的方法,也日益受到关注。其中,挖掘系统数据和重新分类整理的方法是整合系统生物学的基石之一。虽然使用系统的分析方法所付出的巨大努力已取得了良好的效果,但是在系统工作流程的应用中,缺乏合适的分析工具和专用的数据库是一个重大的瓶颈,这一点是显而易见。这篇文章阐述了应用在系统分析中的现代方法和在大规模系统分析和整合中经常遇到的障碍,这些障碍往往易于被忽略,但对系统分析方法的最终结果产生直接影响。由于它的适用范
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