Merging transcriptomics and metabolomics--advances in breast cancer profiling.
Merging transcriptomics and metabolomics--advances in breast cancer profiling.
复制标题
DOI：
10.1186/1471-2407-10-628
复制
发表时间：
2010-11-16
期刊：
影响因子：
3.8
通讯作者：
Gribbestad IS
中科院分区：
文献类型：
--
作者：
Borgan E;Sitter B;Lingjærde OC;Johnsen H;Lundgren S;Bathen TF;Sørlie T;Børresen-Dale AL;Gribbestad IS
结合基因表达微阵列和高分辨率魔角旋转磁共振波谱（HR MAS MRS）的相同的组织样本，使乳腺癌的转录和代谢谱的比较。本研究的目的是探索这两种不同类型的信息相结合的潜力。对46例乳腺癌患者的乳腺癌组织进行了HR MAS MRS分析，随后进行了基因表达微阵列分析。使用两种策略来联合收割机基因表达和代谢数据;首先使用多变量分析来基于基因表达和代谢数据识别不同的组;其次将特定代谢物的水平与转录本相关联，以提出代谢物水平与潜在生物过程之间的联系的新假设。一个平行的研究被设计来解决结合微阵列和HR MAS MRS的实验问题。在第一个策略中，使用微阵列数据和先前报道的分子分类方法，大多数样品被分类为管腔A。基于HR MAS MR谱的分层聚类，确定了管腔A肿瘤的三个亚组。其中一个亚组中的样品，命名为A2，显示出比其他管腔A样品显著更低的葡萄糖和更高的丙氨酸水平，表明这些肿瘤中更高的糖酵解活性。该组还富集了用与细胞周期和DNA修复相关的基因本体论（GO）术语注释的基因。在第二种策略中，研究了肌醇、甘氨酸、牛磺酸、甘油磷酸胆碱、磷酸胆碱、胆碱和肌酸的浓度与过滤的微阵列数据中的所有转录物之间的相关性。与细胞外基质相关的GO术语在与肌醇和牛磺酸相关性最大的基因中富集，而与细胞周期相关的GO术语在与胆碱相关性最大的基因中富集。此外，在HR MAS MRS后，一个转录物子集被鉴定为具有轻微改变的表达，因此从所有其他分析中删除。结合来自同一乳腺癌样本的转录和代谢数据是可行的，可能有助于更精确的乳腺癌亚分类，并揭示代谢和转录水平之间的关系。参见评论：http://www.biomedcentral.com/1741-7015/8/73
Combining gene expression microarrays and high resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) of the same tissue samples enables comparison of the transcriptional and metabolic profiles of breast cancer. The aim of this study was to explore the potential of combining these two different types of information. Breast cancer tissue from 46 patients was analyzed by HR MAS MRS followed by gene expression microarrays. Two strategies were used to combine the gene expression and metabolic data; first using multivariate analyses to identify different groups based on gene expression and metabolic data; second correlating levels of specific metabolites to transcripts to suggest new hypotheses of connections between metabolite levels and the underlying biological processes. A parallel study was designed to address experimental issues of combining microarrays and HR MAS MRS. In the first strategy, using the microarray data and previously reported molecular classification methods, the majority of samples were classified as luminal A. Three subgroups of luminal A tumors were identified based on hierarchical clustering of the HR MAS MR spectra. The samples in one of the subgroups, designated A2, showed significantly lower glucose and higher alanine levels than the other luminal A samples, suggesting a higher glycolytic activity in these tumors. This group was also enriched for genes annotated with Gene Ontology (GO) terms related to cell cycle and DNA repair. In the second strategy, the correlations between concentrations of myo-inositol, glycine, taurine, glycerophosphocholine, phosphocholine, choline and creatine and all transcripts in the filtered microarray data were investigated. GO-terms related to the extracellular matrix were enriched among the genes that correlated the most to myo-inositol and taurine, while cell cycle related GO-terms were enriched for the genes that correlated the most to choline. Additionally, a subset of transcripts was identified to have slightly altered expression after HR MAS MRS and was therefore removed from all other analyses. Combining transcriptional and metabolic data from the same breast carcinoma sample is feasible and may contribute to a more refined subclassification of breast cancers as well as reveal relations between metabolic and transcriptional levels. See Commentary: http://www.biomedcentral.com/1741-7015/8/73
登录
查看更多内容
影响因子：
4.3
作者：
Eden E;Lipson D;Yogev S;Yakhini Z
通讯作者：
Yakhini Z
影响因子：
4.4
作者：
Sørlie T;Wang Y;Xiao C;Johnsen H;Naume B;Samaha RR;Børresen-Dale AL
通讯作者：
Børresen-Dale AL
影响因子：
3.8
作者：
Moestue SA;Borgan E;Huuse EM;Lindholm EM;Sitter B;Børresen-Dale AL;Engebraaten O;Maelandsmo GM;Gribbestad IS
通讯作者：
Gribbestad IS
影响因子：
2.9
作者：
Morse, David L.;Carroll, Danielle;Day, Sam;Gray, Heather;Sadarangani, Pooja;Murthi, Shiva;Job, Constantin;Baggett, Brenda;Raghunand, Natarajan;Gillies, Robert J.
通讯作者：
Gillies, Robert J.
影响因子：
6.4
作者：
Eliyahu, Galit;Kreizman, Tamar;Degani, Hadassa
通讯作者：
Degani, Hadassa