Lists2Networks: integrated analysis of gene/protein lists.
Lists2Networks: integrated analysis of gene/protein lists.
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Lists2Networks：基因/蛋白质列表的综合分析。
DOI：
10.1186/1471-2105-11-87
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发表时间：
2010-02-12
影响因子：
3
通讯作者：
Ma'ayan A
中科院分区：
文献类型：
--
作者：
Lachmann A;Ma'ayan A
系统生物学家面临着分析大规模研究结果的困难，这些研究描述了许多基因、RNA和蛋白质的活性，应用于不同的实验，在不同的条件下，并在不同的出版物中报道。为了应对这一挑战，需要在一个连贯的全球框架中比较不同相关研究的结果，如mRNA表达微阵列、全基因组ChIP-X、RNAi筛选、蛋白质组学和磷酸化蛋白质组学实验。此外，将高内容的多层次实验结果与先前的生物学知识联系起来，对于识别功能主题和形成新的假设是有用的。我们提出了Lists 2Networks，一个基于网络的系统，允许用户将哺乳动物基因/蛋白质的列表上传到一个基于服务器的程序进行综合分析。该系统包括基于网络的工具，以利用不同的集合操作来操纵列表，使用现有的蛋白质-蛋白质相互作用、共表达相关性或背景知识共注释相关性的哺乳动物网络来扩展列表，以及针对现有生物学知识的许多基因列表库应用基因列表富集分析，所述现有生物学知识例如途径、基因本体术语、激酶底物、microRNA-mRAN、以及蛋白质-蛋白质相互作用、代谢物和蛋白质结构域。这样的分析可以针对与特定注释相关联的基因列表的许多现有知识库一次应用于几个列表。该系统还包含允许用户导出网络并与系统的其他用户共享列表的功能。Lists 2Networks是一个用户友好的基于Web的软件系统，预计将显着简化实验系统生物学家在多个层次的监管采用高通量实验的计算分析过程。该系统可在http://www.lists2networks.org上免费获得。
Systems biologists are faced with the difficultly of analyzing results from large-scale studies that profile the activity of many genes, RNAs and proteins, applied in different experiments, under different conditions, and reported in different publications. To address this challenge it is desirable to compare the results from different related studies such as mRNA expression microarrays, genome-wide ChIP-X, RNAi screens, proteomics and phosphoproteomics experiments in a coherent global framework. In addition, linking high-content multilayered experimental results with prior biological knowledge can be useful for identifying functional themes and form novel hypotheses. We present Lists2Networks, a web-based system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. Lists2Networks is a user friendly web-based software system expected to significantly ease the computational analysis process for experimental systems biologists employing high-throughput experiments at multiple layers of regulation. The system is freely available at http://www.lists2networks.org.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
30.8
作者：
Cordeddu, Viviana;Di Schiavi, Elia;Pennacchio, Len A.;Ma'ayan, Avi;Sarkozy, Anna;Fodale, Valentina;Cecchetti, Serena;Cardinale, Alessio;Martin, Joel;Schackwitz, Wendy;Lipzen, Anna;Zampino, Giuseppe;Mazzanti, Laura;Digilio, Maria C.;Martinelli, Simone;Flex, Elisabetta;Lepri, Francesca;Bartholdi, Deborah;Kutsche, Kerstin;Ferrero, Giovanni B.;Anichini, Cecilia;Selicorni, Angelo;Rossi, Cesare;Tenconi, Romano;Zenker, Martin;Merlo, Daniela;Dallapiccola, Bruno;Iyengar, Ravi;Bazzicalupo, Paolo;Gelb, Bruce D.;Tartaglia, Marco
通讯作者：
Tartaglia, Marco
影响因子：
3
作者：
Berger SI;Posner JM;Ma'ayan A
通讯作者：
Ma'ayan A
DOI：
10.1093/bioinformatics/btp026
发表时间：
2009-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lachmann A;Ma'ayan A
通讯作者：
Ma'ayan A
影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R