VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data.
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data.
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DOI：
10.1093/nar/gki443
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发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Subramaniam, S
中科院分区：
文献类型：
--
作者：
Hsiao, A;Ideker, T;Olefsky, JM;Subramaniam, S
微阵列是用于快照细胞和组织的基因表达谱的宝贵的高通量工具。对微阵列数据提出的最基本和最基本的问题之一是，单个基因是否被特定的刺激显著激活或抑制。在此之前，我们已经提出了两种贝叶斯统计方法，统称为带区域指数的方差建模后验推断(吸血鬼)。这些方法都需要一个复杂的建模步骤，然后是后验概率密度的积分。我们在这里提供了一个公开可用的基于Web的平台，允许用户使用吸血鬼统计框架轻松加载数据、关联相关样本并识别差异表达的特征。此外，这套工具无缝地集成了一种新的基因注释工具，称为GOBY，它可以识别在统计上被过度代表的基因组。与这一流派中的其他工具不同，GOBY可以本地化丰富内容，同时尊重基因本体论(GO)等注释系统的层次结构。通过识别GO术语、京都百科全书基因和基因组路径以及TRANSFAC转录因子结合位点的统计显著丰富，用户可以深入了解一组差异表达基因的生理意义。吸血鬼微阵列套件可以在以下位置访问。
Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether individual genes are significantly activated or repressed by a particular stimulus. We have previously presented two Bayesian statistical methods for this level of analysis, collectively known as variance-modeled posterior inference with regional exponentials (VAMPIRE). These methods each require a sophisticated modeling step followed by integration of a posterior probability density. We present here a publicly available, web-based platform that allows users to easily load data, associate related samples and identify differentially expressed features using the VAMPIRE statistical framework. In addition, this suite of tools seamlessly integrates a novel gene annotation tool, known as GOby, which identifies statistically overrepresented gene groups. Unlike other tools in this genre, GOby can localize enrichment while respecting the hierarchical structure of annotation systems like Gene Ontology (GO). By identifying statistically significant enrichment of GO terms, Kyoto Encyclopedia of Genes and Genomes pathways, and TRANSFAC transcription factor binding sites, users can gain substantial insight into the physiological significance of sets of differentially expressed genes. The VAMPIRE microarray suite can be accessed at .
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DOI：
10.1073/pnas.011404098
发表时间：
2001-01-02
影响因子：
11.1
作者：
Li, C;Wong, WH
通讯作者：
Wong, WH
DOI：
10.1073/pnas.091062498
发表时间：
2001-04-24
影响因子：
11.1
作者：
Tusher, VG;Tibshirani, R;Chu, G
通讯作者：
Chu, G
影响因子：
5.8
作者：
Baldi, P;Long, AD
通讯作者：
Long, AD
影响因子：
2.1
作者：
Irizarry, RA;Hobbs, B;Speed, TP
通讯作者：
Speed, TP
影响因子：
5.8
作者：
Beissbarth, T;Speed, TP
通讯作者：
Speed, TP