lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes
lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes
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DOI：
10.1093/bioinformatics/btw017
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发表时间：
2016-05-15
期刊：
影响因子：
5.8
通讯作者：
Zhao, Min
中科院分区：
文献类型：
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作者：
Liu, Yining;Zhao, Min
一个总结：人类长链非编码RNA（longnoncodingRNA，lncRNA）在多种肿瘤的发生、发展过程中发挥着重要作用。然而，绝大多数人类lncRNA的功能仍然难以捉摸。近年来的研究表明，在各种模式生物中，大多数lncRNA的表达水平与其邻近的蛋白质编码基因的表达水平不一致。因此，它可能是有用的，以推断lncRNA的潜在的生物学功能，在癌症的发展，通过更全面的功能视图的共表达的癌症基因超越仅仅物理接近的基因。为此，我们对lncRNA与非相邻癌基因之间的相互作用进行了彻底的搜索和分析，并提供了一个全面的共表达数据资源LnCaNet。在当前版本中，LnCaNet包含在2922个匹配的TCGA样本中预先计算的9641个lncRNA和2544个良好分类的癌症基因的8 494 907个显著共表达对。具体地，我们整合了公共数据库中的10个癌症基因列表，并分别计算了11种TCGA癌症类型中与所有lncRNA的共表达。基于所得到的110个共表达网络，我们确定了11种癌症中与细胞外空间相关的17个共同调控对。我们期望LnCaNet将使研究人员能够探索lncRNA表达模式，其受影响的癌症基因和途径，在特定癌症类型的背景下的生物学意义以及与特定类型的lncRNA-癌症基因相互作用相关的其他有用的注释。
A Summary: Thousands of human long non-coding RNAs (lncRNAs) have been identified in cancers and played important roles in a wide range of tumorigenesis. However, the functions of vast majority of human lncRNAs are still elusive. Emerging studies revealed that the expression level of majority lncRNAs shows discordant expression pattern with their protein-coding gene neighbors in various model organisms. Therefore, it may be useful to infer lncRNAs' potential biological function in cancer development by more comprehensive functional views of co-expressed cancer genes beyond mere physical proximity of genes. To this aim, we performed thorough searches and analyses of the interactions between lncRNA and non-neighboring cancer genes and provide a comprehensive co-expression data resource, LnCaNet. In current version, LnCaNet contains the pre-computed 8 494 907 significant co-expression pairs of 9641 lncRNAs and 2544 well-classified cancer genes in 2922 matched TCGA samples. In detail, we integrated 10 cancer gene lists from public database and calculate the co-expression with all the lncRNAs in 11 TCGA cancer types separately. Based on the resulted 110 co-expression networks, we identified 17 common regulatory pairs related to extracellular space shared in 11 cancers. We expect LnCaNet will enable researcher to explore lncRNA expression pattern, their affected cancer genes and pathways, biological significance in the context of specific cancer types and other useful annotation related to particular kind of lncRNA-cancer gene interaction.