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    Atherosclerosis genes and related reagents and methods of use thereof
    4.
    发明申请
    Atherosclerosis genes and related reagents and methods of use thereof 审中-公开
    动脉粥样硬化基因及相关试剂及其使用方法

    公开(公告)号：US20070253901A1

    公开(公告)日：2007-11-01

    申请号：US11412437

    申请日：2006-04-27

    申请人： David Deng ,  Anya Tsalenko ,  Amir Ben-Dor ,  Zohar Yakhini ,  Thomas Quertermous ,  Euan Ashley ,  Eugene Yang ,  Raymond Tabibiazar ,  Philip Tsao

    发明人： David Deng ,  Anya Tsalenko ,  Amir Ben-Dor ,  Zohar Yakhini ,  Thomas Quertermous ,  Euan Ashley ,  Eugene Yang ,  Raymond Tabibiazar ,  Philip Tsao

    IPC分类号： A61K51/00 ,  A61K49/10 ,  C07K16/46 ,  C07K14/54

    CPC分类号： G01N33/6893 ,  G01N2800/323

    摘要： The invention provides genes (DEA genes) that are differentially expressed in atherosclerotic lesions and polypeptides encoded by these genes. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one a DEA gene. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to atherosclerosis involving detecting expression or activity of an expression product of one or more of the DEA genes. The invention further provides therapeutic methods comprising administering to a subject a composition comprising a targeting agent conjugated to a functional moiety that binds selectively binds to a polypeptide encoded by a DEA gene.

    摘要翻译： 本发明提供在动脉粥样硬化病变和由这些基因编码的多肽中差异表达的基因（DEA基因）。 本发明提供了包含与功能部分缀合的靶向剂的组合物，其中所述靶向剂选择性地结合由DEA基因之一编码的多肽。 功能部分可以是显像剂，治疗剂等。本发明还提供了提供涉及检测一种或多种DEA基因的表达产物的表达或活性的动脉粥样硬化相关的诊断或预后信息的方法。 本发明进一步提供治疗方法，包括向受试者施用包含与功能性部分缀合的靶向试剂的组合物，其结合选择性结合由DEA基因编码的多肽。

    Method and system for computational detection of common aberrations from multi-sample comparative genomic hybridization data sets
    5.
    发明申请
    Method and system for computational detection of common aberrations from multi-sample comparative genomic hybridization data sets 审中-公开
    用于多样本比较基因组杂交数据集的常见像差的计算检测方法和系统

    公开(公告)号：US20070203653A1

    公开(公告)日：2007-08-30

    申请号：US11363699

    申请日：2006-02-28

    申请人： Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson ,  Zohar Yakhini

    发明人： Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson ,  Zohar Yakhini

    IPC分类号： G06F19/00

    CPC分类号： G16B25/00 ,  G16B30/00 ,  G16B40/00

    摘要： Various embodiments of the present invention are directed to methods and systems for automatic, statistically meaningful detection of aberrations common to multiple samples within a sample set. Many various aberration-calling techniques are used to identify aberrant intervals within each of the samples of the sample set. A set of candidate intervals is constructed to include the aberrant intervals identified by the aberration-calling technique, as well as two-way intersections of the identified aberrant intervals. A score indicating the statistical relevance of each candidate interval with respect to each sample is next assigned to each candidate interval. Then, a total significance score is assigned to each candidate interval based on the individual scores for the candidate interval with respect to each sample. The most statistically significant candidate intervals may be selected based on the total significance scores assigned to the candidate intervals.

    摘要翻译： 本发明的各种实施例涉及用于对样本集合内的多个样本共同的像差进行自动统计学上有意义的检测的方法和系统。 使用许多各种像差调用技术来识别样本集合的每个样本内的异常间隔。 一组候选间隔被构造成包括由像差调用技术识别的异常间隔以及所识别的异常间隔的双向交叉。 指示每个候选间隔相对于每个样本的统计学相关性的分数接下来分配给每个候选间隔。 然后，基于针对每个样本的候选间隔的各个评分，将总重要性得分分配给每个候选间隔。 可以基于分配给候选间隔的总重要性得分来选择最具统计意义的候选间隔。

    Analyzing and visualizing enrichment in DNA sequence alterations
    6.
    发明申请
    Analyzing and visualizing enrichment in DNA sequence alterations 审中-公开
    分析和可视化DNA序列变异中的富集

    公开(公告)号：US20060173635A1

    公开(公告)日：2006-08-03

    申请号：US11049565

    申请日：2005-02-01

    申请人： Zohar Yakhini ,  Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson

    发明人： Zohar Yakhini ,  Amir Ben-Dor ,  Anya Tsalenko ,  Doron Lipson

    IPC分类号： G06F19/00

    CPC分类号： G16B25/00 ,  G16B20/00

    摘要： Methods, tools, systems and computer readable media for analyzing CGH data, together with data from an independent source. Independent data is compared with the CGH data, wherein the CGH data is characterized by sets of defined regions differentiated by at least one property. Enrichment is assessed for at least one subset of the data from an independent source with regard to at least one of the sets of defined regions in the CGH data. Methods, tools, systems and computer readable media for visualizing CGH data as it is impacted by data from an independent source are also provided. A relationship between at least one defined set of the CGH data and at least one set of sequence elements defined in the data from an independent source may be visualized.

    摘要翻译： 用于分析CGH数据的方法，工具，系统和计算机可读介质，以及来自独立源的数据。 将独立数据与CGH数据进行比较，其中CGH数据由通过至少一个属性区分的限定区域的集合来表征。 相对于CGH数据中的至少一个限定区域的集合，来自独立源的至少一个数据子集的浓度被评估。 还提供了用于可视化CGH数据的方法，工具，系统和计算机可读介质，因为它受来自独立源的数据的影响。 至少一个定义的CGH数据集与来自独立源的数据中定义的至少一组序列元素之间的关系可以被可视化。

    Method and system for analysis of gene-expression data
    8.
    发明申请
    Method and system for analysis of gene-expression data 审中-公开
    用于分析基因表达数据的方法和系统

    公开(公告)号：US20060190190A1

    公开(公告)日：2006-08-24

    申请号：US11048970

    申请日：2005-02-02

    申请人： Zohar Yakhini ,  Amir Ben-Dor ,  Anya Tsalenko ,  David Deng

    发明人： Zohar Yakhini ,  Amir Ben-Dor ,  Anya Tsalenko ,  David Deng

    IPC分类号： G06F19/00

    CPC分类号： G16B25/00

    摘要： In various embodiments of the present invention, initial gene-expression data is initially partitioned into classes by patient, subject, or other identifier of a source of samples, expression-level-differences are computed for each gene with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for each gene from the expression-level difference metrics computed for each initial partition. In other words, rather than partitioning gene-expression-level data directly into two or more classes relative to an event of interest, the gene-expression-level data is first partitioned according to sample source, and then each sample-source partition is partitioned into two or more classes relative to an event of interest. Levels of significance, or p-values, can be straightforwardly computed for both rank consistency scores and fold-change consistency scores.

    摘要翻译： 在本发明的各种实施方案中，初始基因表达数据最初按照样品来源的患者，受试者或其他标识符分类，根据每个初始分区计算每个基因的表达水平差异， 根据为每个初始分区计算的表达级差异度量，为每个基因计算排序一致性分数或倍数变化一致性分数。 换句话说，不是将基因表达级数据直接分为两个或更多相关于感兴趣事件的类别，因此首先根据样本源分割基因表达级数据，然后将每个样本源分区分区 相对于感兴趣的事件进入两个或更多个类。 对于等级一致性分数和折叠一致性分数，可以直接计算重要程度或p值。

    Method and system for analysis of biological and chemical data
    9.
    发明申请
    Method and system for analysis of biological and chemical data 审中-公开
    生物和化学数据分析方法和系统

    公开(公告)号：US20050273269A1

    公开(公告)日：2005-12-08

    申请号：US10863045

    申请日：2004-06-07

    申请人： Zohar Yakhini ,  Anya Tsalenko ,  Amir Ben-Dor

    发明人： Zohar Yakhini ,  Anya Tsalenko ,  Amir Ben-Dor

    IPC分类号： G01N33/48 ,  G01N33/50 ,  G06F19/00

    CPC分类号： G16B40/00 ,  G16B25/00 ,  G16B45/00

    摘要： In various embodiments of the present invention, initial experimental data is initially partitioned into classes by sample source, concentration or number-of-molecule values are computed with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for various molecular concentration or number-of-copies determinants with respect to one or more class-specifying events of interest. In other words, rather than partitioning experimental data directly into two or more classes relative to an event of interest, the experimental data is first partitioned according to sample source, and then each sample-source partition is partitioned into two or more classes relative to an event of interest.

    摘要翻译： 在本发明的各种实施方案中，初始实验数据最初通过样品源分成类别，相对于每个初始分区计算浓度或分子数值，并计算等级一致性分数或折叠变化一致性分数 对于关于一个或多个感兴趣的类别指定事件的各种分子浓度或拷贝数决定因素。 换句话说，相对于感兴趣的事件，实验数据直接分成两个或更多个类，而不是根据样本源对实验数据进行分区，然后将每个样本源分区分为两个或更多个类 感兴趣的事件

    Systems and methods for determining cell type composition of mixed cell populations using gene expression signatures
    10.
    发明申请
    Systems and methods for determining cell type composition of mixed cell populations using gene expression signatures 审中-公开
    使用基因表达特征确定混合细胞群体的细胞类型组成的系统和方法

    公开(公告)号：US20050048463A1

    公开(公告)日：2005-03-03

    申请号：US10841164

    申请日：2004-05-07

    申请人： David Deng ,  Anya Tsalenko ,  Zohar Yakhini ,  Laurakay Bruhn ,  Amir Ben-Dor

    发明人： David Deng ,  Anya Tsalenko ,  Zohar Yakhini ,  Laurakay Bruhn ,  Amir Ben-Dor

    IPC分类号： C12Q1/68 ,  C12Q1/70 ,  G06F19/00

    CPC分类号： G16B40/00 ,  G16B25/00

    摘要： The present invention provides systems and methods for determining the cell type composition of a mixed cell population. The invention provides systems and methods for identifying and defining pure cell type specific signatures. These pure cell type specific signatures may be used to determine the cell type composition of a mixed cell population. The systems and methods of the invention may be used for a variety of research and clinical purposes. For example, they may be used to detect the presence or absence of cells of particular types, and to determine whether variations in gene expression, e.g., between different samples, represent true changes in gene expression or differences in cell type composition of the samples.

    摘要翻译： 本发明提供了用于确定混合细胞群体的细胞类型组成的系统和方法。 本发明提供用于识别和定义纯细胞类型特异性特征的系统和方法。 这些纯细胞类型特异性标记可用于确定混合细胞群体的细胞类型组成。 本发明的系统和方法可用于各种研究和临床目的。 例如，它们可以用于检测特定类型的细胞的存在或不存在，并且确定基因表达的变化，例如不同样品之间的变化是否代表基因表达的真实变化或样品的细胞类型组成的差异。