Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies.
Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies.
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DOI：
10.1186/1471-2164-14-35
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发表时间：
2013-01-16
期刊：
影响因子：
4.4
通讯作者：
Wong L
中科院分区：
文献类型：
--
作者：
Goh WW;Fan M;Low HS;Sergot M;Wong L
蛋白质组学特征分析（PSP）是一种新的基于命中率的方法，被证明在解决蛋白质组学中的一致性和覆盖率问题上是有用的。作为一项后续研究，有几点需要解决：1/ PSP对通路的普适性，2/理解在我们的肝癌数据集中共同位于相同通路上的重要复合物和通路之间的生物学相互作用，3/了解PSP的假阳性率和4/证明PSP适用于其他合适的蛋白质组学数据集，并通过使用专门的本体来扩展PSP的分析分辨率。1/ PSP在Pathway-Derived Subnets（PDS）中表现良好。比较来自各种途径数据库的PDS的性能，我们发现，一个综合的方法是最好的优化分析分辨率。特征选择还证实了显著的PDS与癌症表型密切相关。2/在肝癌中，对共同定位在相同途径上的重要PSP复合物和PDS的相关性研究揭示了嘌呤代谢途径与参与DNA修复的其他两种复合物之间的有趣关系。我们的工作表明，进展到贫穷阶段需要额外的突变，破坏DNA修复酶。3/假阳性分析表明，PSP，适用于复合物和PDS，是强大的和精确的。4/通过专家策划的脂质本体论，我们发现了几种有趣的脂质相关复合物，它们可能与癌症进展有关。特别感兴趣的是HMGB 1-HMGB 2-HSC 70-ERP 60-GAPDH复合物，其也参与DNA修复。我们还使用非小细胞肺癌数据集证明了PSP的普遍性。PSP是一种强大而精确的技术，能够识别生物学上连贯的特征。它适用于生物复合体，网络预测集群以及PDS。在这里，一个重要的PDS和复合物之间的相互作用的实例，可能显着参与肝癌的进展，但还没有很好地理解，证明。还证明了PSP的分析分辨率使用专门的本体增强。
Proteomics Signature Profiling (PSP) is a novel hit-rate based method that proved useful in resolving consistency and coverage issues in proteomics. As a follow-up study, several points need to be addressed: 1/ PSP’s generalisability to pathways, 2/ understanding the biological interplay between significant complexes and pathway subnets co-located on the same pathways on our liver cancer dataset, 3/ understanding PSP’s false positive rate and 4/ demonstrating that PSP works on other suitable proteomics datasets as well as expanding PSP’s analytical resolution via the use of specialised ontologies. 1/ PSP performs well with Pathway-Derived Subnets (PDSs). Comparing the performance of PDSs derived from various pathway databases, we find that an integrative approach is best for optimising analytical resolution. Feature selection also confirms that significant PDSs are closely connected to the cancer phenotype. 2/ In liver cancer, correlation studies of significant PSP complexes and PDSs co-localised on the same pathways revealed an interesting relationship between the purine metabolism pathway and two other complexes involved in DNA repair. Our work suggests progression to poor stage requires additional mutations that disrupt DNA repair enzymes. 3/ False positive analysis reveals that PSP, applied on both complexes and PDSs, is powerful and precise. 4/ Via an expert-curated lipid ontology, we uncovered several interesting lipid-associated complexes that could be associated with cancer progression. Of particular interest is the HMGB1-HMGB2-HSC70-ERP60-GAPDH complex which is also involved in DNA repair. We also demonstrated generalisability of PSP using a non-small-cell lung carcinoma data set. PSP is a powerful and precise technique, capable of identifying biologically coherent features. It works with biological complexes, network-predicted clusters as well as PDSs. Here, an instance of the interplay between significant PDSs and complexes, possibly significantly involved in liver cancer progression but not well understood as yet, is demonstrated. Also demonstrated is the enhancement of PSP’s analytical resolution using specialised ontologies.
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影响因子：
9.9
作者：
通讯作者：
--
影响因子：
3
作者：
Soh D;Dong D;Guo Y;Wong L
通讯作者：
Wong L
影响因子：
4.4
作者：
Wei, Yuhong;Tong, Jiefei;Moran, Michael F.
通讯作者：
Moran, Michael F.
影响因子：
9.9
作者：
通讯作者：
--
DOI：
10.1073/pnas.1118455109
发表时间：
2012-02-14
影响因子：
11.1
作者：
Pang, Bo;McFaline, Jose L.;Dedon, Peter C.
通讯作者：
Dedon, Peter C.