Extracting consistent knowledge from highly inconsistent cancer gene data sources.
Extracting consistent knowledge from highly inconsistent cancer gene data sources.
复制标题
从高度不一致的癌症基因数据源中提取一致的知识
DOI：
10.1186/1471-2105-11-76
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发表时间：
2010-02-05
影响因子：
3
通讯作者：
Guo Z
中科院分区：
文献类型：
--
作者：
Gong X;Wu R;Zhang Y;Zhao W;Cheng L;Gu Y;Zhang L;Wang J;Zhu J;Guo Z
背景数百个与肿瘤发生有因果关系的基因已被发现并收集在各种数据库中。为了有效地应用这些丰富的，但不同的数据源，它是至关重要的，以评估其consistency.ResultsFirst，我们发现，从一些主要的数据源的癌症基因的列表是高度不一致的重叠基因。特别是，在以前的小规模研究中积累的大多数癌症基因在当前的高通量基因组筛选研究中无法重新发现。然后，基于本研究中提出的度量，我们表明来自不同数据源的大多数癌症基因列表在功能上高度一致。最后，我们从各种数据源中提取功能一致的癌症基因，并将其收集在我们的数据库F-Census.ConclusionsAlthough他们有很低的基因重叠，大多数癌症基因数据源是高度一致的功能水平，这表明他们可以单独捕获部分基因在一些关键途径与癌症。我们的研究结果表明，目前用于癌症研究的样本量可能不足以持续捕获单个癌症基因，但可能足以找到一些在功能上代表大多数癌症基因的癌症基因。F-Census数据库为生物学家提供了一个有用的工具，用于从各种数据源中浏览和提取功能一致的癌症基因。
BackgroundHundreds of genes that are causally implicated in oncogenesis have been found and collected in various databases. For efficient application of these abundant but diverse data sources, it is of fundamental importance to evaluate their consistency.ResultsFirst, we showed that the lists of cancer genes from some major data sources were highly inconsistent in terms of overlapping genes. In particular, most cancer genes accumulated in previous small-scale studies could not be rediscovered in current high-throughput genome screening studies. Then, based on a metric proposed in this study, we showed that most cancer gene lists from different data sources were highly functionally consistent. Finally, we extracted functionally consistent cancer genes from various data sources and collected them in our database F-Census.ConclusionsAlthough they have very low gene overlapping, most cancer gene data sources are highly consistent at the functional level, which indicates that they can separately capture partial genes in a few key pathways associated with cancer. Our results suggest that the sample sizes currently used for cancer studies might be inadequate for consistently capturing individual cancer genes, but could be sufficient for finding a number of cancer genes that could represent functionally most cancer genes. The F-Census database provides biologists with a useful tool for browsing and extracting functionally consistent cancer genes from various data sources.
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影响因子：
15.8
作者：
Chan, Timothy A.;Glockner, Sabine;Yi, Joo Mi;Chen, Wei;Van Neste, Leander;Cope, Leslie;Herman, James G.;Velculescu, Victor;Schuebel, Kornel E.;Ahuja, Nita;Baylin, Stephen B.
通讯作者：
Baylin, Stephen B.
影响因子：
3
作者：
Chua HN;Sung WK;Wong L
通讯作者：
Wong L
影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
DOI：
10.1038/nrc1299
发表时间：
2004-03
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
通讯作者：
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候选癌基因的优先级 - 对致癌研究的帮助。
影响因子：
14.9
作者：
Furney, Simon J.;Calvo, Borja;Larranaga, Pedro;Lozano, Jose A.;Lopez-Bigas, Nuria
通讯作者：
Lopez-Bigas, Nuria