TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
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DOI：
10.1371/journal.pone.0004001
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发表时间：
2008
期刊：
影响因子：
3.7
通讯作者：
Puthier D
中科院分区：
文献类型：
--
作者：
Lopez F;Textoris J;Bergon A;Didier G;Remy E;Granjeaud S;Imbert J;Nguyen C;Puthier D
随着公共微阵列存储库不断增长，我们面临着设计策略以提供可用数据的挑战。
我们使用Markov聚类算法的修改版本从存储在基因表达式Omnibus数据库中的数百个微阵列数据集中的数百个微阵列数据集（n = 1,484）中提取了共同调节基因的簇（TS）。使用David知识库测试了功能性的富集Java应用程序，带有开放式插件体系结构的Tbrowser，其接口实现了高度复杂的搜索引擎，支持了几个布尔运算符（http://tagc.univ-mrs.fr/tbrowser/）。包含标识符列表（基因符号或affyids）或与一组功能术语相关联。
作为原理的证明，Tbrowser用于定义乳腺癌细胞特异性基因，并检测肿瘤中的染色体异常，利用我们的大量转录特征，我们构建了一张综合的地图所有在HGU133A Affymetrix平台上进行的实验。
As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms. As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
4.1
作者：
Lacroix, M;Leclercq, G
通讯作者：
Leclercq, G
DOI：
10.1111/j.1600-0749.2007.00375.x
发表时间：
2007-06-01
期刊：
PIGMENT CELL RESEARCH
影响因子：
--
作者：
Johansson, Peter;Pavey, Sandra;Hayward, Nicholas
通讯作者：
Hayward, Nicholas
影响因子：
3.1
作者：
Lattimore, BS;van Dongen, S;Crabbe, MJC
通讯作者：
Crabbe, MJC
NCBI GEO：开采数以百万计的表达概况 - 数据库和工具更新。
影响因子：
14.9
作者：
Barrett, Tanya;Troup, Dennis B.;Wilhite, Stephen E.;Ledoux, Pierre;Rudnev, Dmitry;Evangelista, Carlos;Kim, Irene F.;Soboleva, Alexandra;Tomashevsky, Maxim;Edgar, Ron
通讯作者：
Edgar, Ron