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1. 发明申请

WO2005088306A3 BIOLOGICALLY-ACTIVE DNA-BINDING SITES AND RELATED METHODS 审中-公开
标题翻译：生物活性DNA结合位点和相关方法
公开(公告)号：WO2005088306A3
公开(公告)日：2005-11-03
申请号：PCT/US2005007249
申请日：2005-03-03
申请人： WHITEHEAD BIOMEDICAL INST , HARBISON CHRISTOPHER , YOUNG RICHARD A , GORDON DAVID B , FRAENKEL ERNEST
发明人： HARBISON CHRISTOPHER , YOUNG RICHARD A , GORDON DAVID B , FRAENKEL ERNEST
IPC分类号： C12Q1/68 , G01N33/53
CPC分类号： G01N33/5308 , C12Q2522/00
摘要： The invention relates to the identification of biologically-active DNA-binding sites to which a protein of interest binds in a cell. The invention also relates to the identification of agents and conditions which alter the biologically-active DNA-binding sites to which a protein binds. One aspect of the invention also provides methods for identifying pathways that are regulated by transcriptional regulators and for modulating the activity of the pathways.
摘要翻译：本发明涉及鉴定感兴趣的蛋白质在细胞中结合的生物活性DNA结合位点。本发明还涉及鉴定改变蛋白质结合的生物活性DNA结合位点的试剂和条件。本发明的一个方面还提供了用于鉴定受转录调节因子调节的途径和用于调节途径活性的途径的方法。

2. 发明申请

WO2017027559A1 SYSTEMS, APPARATUS, AND METHODS FOR ANALYZING AND PREDICTING CELLULAR PATHWAYS 审中-公开
标题翻译：用于分析和预测细胞途径的系统，装置和方法
公开(公告)号：WO2017027559A1
公开(公告)日：2017-02-16
申请号：PCT/US2016/046289
申请日：2016-08-10
申请人： MASSACHUSETTS INSTITUTE OF TECHNOLOGY , PIRHAJI, Leila , FRAENKEL, Ernest
发明人： PIRHAJI, Leila , FRAENKEL, Ernest
IPC分类号： G06F19/10 , G06F19/12 , G06F19/18 , G06F19/24 , G06F19/26 , G06F19/28
CPC分类号： G06F19/12 , G01N33/5038 , G01N33/6848 , G01N33/6896 , G01N2800/2835 , G06F19/18
摘要： Integrative analysis of metabolites is essential to obtain a comprehensive view of dysregulated biological pathways leading to a disease. Despite the great potential of metabolites their system level analysis has been limited. Global measurements of the metabolites by liquid chromatography-mass spectrometry (MS) detects metabolites features changing in a disease. However, identification of each feature is a bottleneck in metabolomics, in which a fraction of them are identified via tandem MS. Consequently, the scarcity of these data add additional barriers to decipher their biological meaning, especially in relation to other 'omic data such as proteomics. To address these challenges, a novel network-based approach called PIUMet is described. PIUMet infers dysregulated pathways and components from the differential metabolite features between control and disease systems without the need for the prior identification. The application of PIUMet is demonstrated by integrative analysis of untargeted lipid profiling data of a cell line model of Huntington's disease. The results show that PIUMet inferred dysregulation of sphingolipid metabolism in the disease cells. Additionally, PIUMet identified disease-modifying metabolite in the pathway that remained undetected experimentally. Furthermore, the lipidomic data of these cell lines was integrated with global phospho-proteomic ones. Integrative analysis of these data using PIUMet was shown to systematically lead to identifying dysregulated proteins in the disease cells that cannot be distinguished with individual analysis of each dataset.
摘要翻译：代谢物的综合分析对于获得导致疾病的失调生物学途径的综合观点至关重要。尽管代谢物的潜力很大，但其系统水平分析却受到限制。通过液相色谱 - 质谱法（MS）对代谢物进行全球测量可以检测出疾病发生变化的代谢物特征。然而，每个特征的识别是代谢组学的瓶颈，其中一部分通过串联MS鉴定。因此，这些数据的稀缺性增加了破坏其生物学意义的更多障碍，特别是与其他“蛋白质组学”等数据相关。为了解决这些挑战，描述了一种称为PIUMet的新颖的基于网络的方法。 PIUMet推测控制和疾病系统之间差异代谢特征的失调途径和成分，而不需要先前的鉴定。通过对亨廷顿舞蹈病细胞系模型的非靶向脂质分析数据的综合分析证明了PIUMet的应用。结果表明，PIUMet推测疾病细胞中鞘脂代谢紊乱。此外，PIUMet确定了通路中的疾病修复代谢物，在实验中未被发现。此外，这些细胞系的脂质组学数据与全球磷蛋白质组合。显示了使用PIUMet的这些数据的综合分析，以系统地导致识别疾病细胞中的失调蛋白质，这些蛋白质不能用每个数据集的个体分析来区分。

3. 发明申请

WO2005088306A2 BIOLOGICALLY-ACTIVE DNA-BINDING SITES AND RELATED METHODS 审中-公开
标题翻译：生物活性DNA结合位点及相关方法
公开(公告)号：WO2005088306A2
公开(公告)日：2005-09-22
申请号：PCT/US2005/007249
申请日：2005-03-03
申请人： WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH , HARBISON, Christopher , YOUNG, Richard, A. , GORDON, David, B. , FRAENKEL, Ernest
发明人： HARBISON, Christopher , YOUNG, Richard, A. , GORDON, David, B. , FRAENKEL, Ernest
IPC分类号： G01N33/53
CPC分类号： G01N33/5308 , C12Q2522/00
摘要： The invention relates to the identification of biologically-active DNA-binding sites to which a protein of interest binds in a cell. The invention also relates to the identification of agents and conditions which alter the biologically-active DNA-binding sites to which a protein binds. One aspect of the invention also provides methods for identifying pathways that are regulated by transcriptional regulators and for modulating the activity of the pathways.
摘要翻译：本发明涉及鉴定目的蛋白质在细胞中结合的生物活性DNA结合位点。本发明还涉及改变蛋白质结合的生物活性DNA结合位点的试剂和条件的鉴定。本发明的一个方面还提供了鉴定通过转录调节因子调节并调节途径活性的途径的方法。

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