SWIM: a computational tool to unveiling crucial nodes in complex biological networks.
SWIM: a computational tool to unveiling crucial nodes in complex biological networks.
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DOI：
10.1038/srep44797
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发表时间：
2017-03-20
影响因子：
4.6
通讯作者：
Farina L
中科院分区：
文献类型：
--
作者：
Paci P;Colombo T;Fiscon G;Gurtner A;Pavesi G;Farina L
SWItchMiner(SWIM)是前面描述的过程的向导式软件实现，能够提取复杂网络中包含的信息。具体地说，SWIFE发现了一类新的中心，称为“搏击俱乐部中心”，其特征是与最接近的邻居之间存在显著的负相关。其中，一个特殊的基因子集，称为“开关基因”，似乎以一种不寻常的模块内和模块间连接的模式为特征，赋予它们一个关键的拓扑角色，有趣的是，它们的临床-生物学相关性的证据也反映了这一点。在这里，我们将SWIFE应用于癌症基因组图谱中的一大组癌症数据集，以突出可能与癌症发展引起的细胞或组织生理状态的剧烈变化密切相关的开关基因。我们发现，在我们研究的所有癌症中都发现了开关基因，它们包括蛋白质编码基因和非编码RNA，恢复了许多已知的关键癌症参与者，但也恢复了许多尚未在癌症背景下表征的新的潜在生物标记物。此外，SWIM能够在不同的生物体和细胞条件下检测到开关基因，有可能在生物相关的情况下发现重要的参与者，包括但不限于人类癌症。
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called “fight-club hubs”, characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called “switch genes”, appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance. Here, we applied SWIM to a large panel of cancer datasets from The Cancer Genome Atlas, in order to highlight switch genes that could be critically associated with the drastic changes in the physiological state of cells or tissues induced by the cancer development. We discovered that switch genes are found in all cancers we studied and they encompass protein coding genes and non-coding RNAs, recovering many known key cancer players but also many new potential biomarkers not yet characterized in cancer context. Furthermore, SWIM is amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human cancer.