BiologicalNetworks 2.0--an integrative view of genome biology data.
BiologicalNetworks 2.0--an integrative view of genome biology data.
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DOI：
10.1186/1471-2105-11-610
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发表时间：
2010-12-29
影响因子：
3
通讯作者：
Baitaluk M
中科院分区：
文献类型：
--
作者：
Kozhenkov S;Dubinina Y;Sedova M;Gupta A;Ponomarenko J;Baitaluk M
生物体发育机制研究中的一个重要问题是阐明影响生物体不同水平的相关因素，如基因、生物分子、细胞和细胞系统。这些子系统中存在的众多异构数据源仍然没有充分整合，使研究人员有机会在同一研究框架中一起分析它们。数据综合方法的系统应用也受到综合数据的正交性和命名问题等众多因素的阻碍。在这里，我们报告了一个新版本的BiologicalNetworks，一个研究环境，用于异构生物数据的整体可视化和分析。BiologicalNetworks可以查询数千种不同类型的生物实体（基因/蛋白质，启动子，COG，途径，结合位点等）及其关系（相互作用，共同表达，共同引用等）的属性。该系统包括用于高通量实验中分子相互作用/关系和模块发现的构建途径基础设施。在BiologicalNetworks中还实现了Integrated Genome Viewer和Comparative Genomics Browser应用程序，该应用程序允许搜索和分析基因调控区域及其在多个物种中的保护，以及分子途径/网络，实验数据和功能注释。新版本的BiologicalNetworks及其后端数据库引入了广泛的功能，可以更有效地对微阵列、序列、监管和其他数据进行多层次的综合分析。BiologicalNetworks可在http://www.biologicalnetworks.org上免费获得。
A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other) and their relations (interactions, co-expression, co-citations, and other). The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.
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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
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通讯作者：
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影响因子：
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作者：
Baitaluk, M;Qian, XF;Gupta, A
通讯作者：
Gupta, A
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影响因子：
14.9
作者：
Matys V;Kel-Margoulis OV;Fricke E;Liebich I;Land S;Barre-Dirrie A;Reuter I;Chekmenev D;Krull M;Hornischer K;Voss N;Stegmaier P;Lewicki-Potapov B;Saxel H;Kel AE;Wingender E
通讯作者：
Wingender E