STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.
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DOI：
10.1186/1471-2105-10-332
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发表时间：
2009-10-14
影响因子：
3
通讯作者：
VanBuren V
中科院分区：
文献类型：
--
作者：
Jupiter D;Chen H;VanBuren V
虽然表达微阵列已经成为生物学家使用的标准工具，但对微阵列实验产生的数据进行分析仍然存在挑战。来自不同平台、生物体和实验室的数据比较可能涉及复杂的数据处理，并且推断基因之间的关系仍然很困难。STARNET 2是一个新的基于网络的工具，它允许对来自表达微阵列数据的相关性进行事后视觉分析。STARNET 2有助于用户发现各种物种（人、大鼠、小鼠、鸡、斑马鱼、果蝇、C. elegans，S.酿酒酵母，拟南芥和水稻）通过绘制基因的网络，这些基因在一个大的异质组的预选微阵列实验中紧密共表达。对于每种代表的生物体，从NCBI的Gene Expression Omnibus中检索选定的Affytechnology平台的原始微阵列数据。分别计算在每个平台上测量的表达谱的所有成对Pearson相关系数。这些预编译的结果存储在MySQL数据库中，并由从NCBI检索的其他数据补充。一个基于网络的工具允许用户指定的查询数据库，集中在一个基因的兴趣。查询的结果包括相关网络的图、涉及存在于相关网络中的基因和基因产物的已知相互作用的图以及初始统计分析。两个分析可以并行执行，以比较网络，这是由新的HEATSEEKER模块促进。STARNET 2是一个有用的工具，用于开发关于基因和基因产物之间调控关系的新假设，并已覆盖10个物种。相关性网络的解释支持与先前记录的相互作用的数据库，基因本体论术语的富集测试，以及可用于比较两个网络的相关性距离的热图。STARNET网络中的基因列表可能有助于开发用于因果网络推理的候选基因列表。该工具可在免费获得，不需要用户注册。
Although expression microarrays have become a standard tool used by biologists, analysis of data produced by microarray experiments may still present challenges. Comparison of data from different platforms, organisms, and labs may involve complicated data processing, and inferring relationships between genes remains difficult. STARNET 2 is a new web-based tool that allows post hoc visual analysis of correlations that are derived from expression microarray data. STARNET 2 facilitates user discovery of putative gene regulatory networks in a variety of species (human, rat, mouse, chicken, zebrafish, Drosophila, C. elegans, S. cerevisiae, Arabidopsis and rice) by graphing networks of genes that are closely co-expressed across a large heterogeneous set of preselected microarray experiments. For each of the represented organisms, raw microarray data were retrieved from NCBI's Gene Expression Omnibus for a selected Affymetrix platform. All pairwise Pearson correlation coefficients were computed for expression profiles measured on each platform, respectively. These precompiled results were stored in a MySQL database, and supplemented by additional data retrieved from NCBI. A web-based tool allows user-specified queries of the database, centered at a gene of interest. The result of a query includes graphs of correlation networks, graphs of known interactions involving genes and gene products that are present in the correlation networks, and initial statistical analyses. Two analyses may be performed in parallel to compare networks, which is facilitated by the new HEATSEEKER module. STARNET 2 is a useful tool for developing new hypotheses about regulatory relationships between genes and gene products, and has coverage for 10 species. Interpretation of the correlation networks is supported with a database of previously documented interactions, a test for enrichment of Gene Ontology terms, and heat maps of correlation distances that may be used to compare two networks. The list of genes in a STARNET network may be useful in developing a list of candidate genes to use for the inference of causal networks. The tool is freely available at , and does not require user registration.
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影响因子：
14.9
作者：
Jensen LJ;Kuhn M;Stark M;Chaffron S;Creevey C;Muller J;Doerks T;Julien P;Roth A;Simonovic M;Bork P;von Mering C
通讯作者：
von Mering C
影响因子：
2.6
作者：
Dougherty ER
通讯作者：
Dougherty ER
使用微阵列之间的距离评估微阵列实验中的统计显着性。
影响因子：
3.7
作者：
Hayden D;Lazar P;Schoenfeld D;Inflammation and the Host Response to Injury Investigators
通讯作者：
Inflammation and the Host Response to Injury Investigators
影响因子：
4.3
作者：
Hudson NJ;Reverter A;Dalrymple BP
通讯作者：
Dalrymple BP
影响因子：
5.8
作者：
Husmeier, D
通讯作者：
Husmeier, D