Potential role of chimeric genes in pathway-related gene co-expression modules.
Potential role of chimeric genes in pathway-related gene co-expression modules.
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嵌合基因在通路相关基因共表达模块中的潜在作用
DOI：
10.1186/s12957-021-02248-9
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发表时间：
2021-05-12
影响因子：
3.2
通讯作者：
Ma L
中科院分区：
文献类型：
--
作者：
Li P;Li Y;Ma L
基因融合具有表观遗传修饰功能。基因融合产物编码的新蛋白质在癌症的发展中发挥了作用。因此，更好地了解这些新的蛋白质产品可能会为肿瘤的发病机制提供更多的见解。然而，嵌合基因的特征很少被研究。在这里，我们使用加权共表达网络分析来研究嵌合基因的生物学作用和潜在的机制。下载猪转录组数据，从688个序列和153个样本中筛选嵌合基因和亲本基因，预测它们的结构域，并分析它们之间的关联。我们构建了猪嵌合基因的共表达网络，并利用David对生成的模块进行了基因本体丰富和京都百科全书中的基因和基因组路径分析，以确定与嵌合基因相关的关键网络和模块。我们的发现表明，嵌合基因的大部分蛋白结构域来自融合的前基因。嵌合基因在参与细胞增殖负调控和蛋白质定位到中心体的模块中得到丰富。此外，嵌合基因还与调节细胞生长和分化的生长因子-β超家族有关。此外，在辅助性T细胞中，嵌合基因调节T细胞受体的特异性识别，这意味着嵌合基因在T细胞的调节途径中发挥关键作用。嵌合基因可以产生新的结构域，一些嵌合基因在通路相关功能中起着关键作用。大多数嵌合基因都显示出结合活性。嵌合基因的结构域来自几种亲本基因的组合。嵌合基因在几种细胞通路的调控中起着关键作用。我们的发现可能为探索嵌合基因在肿瘤中的作用提供新的方向。网上版载有补充材料，可在10.1186/s12957-021-02248-9查阅。
Gene fusion has epigenetic modification functions. The novel proteins encoded by gene fusion products play a role in cancer development. Therefore, a better understanding of the novel protein products may provide insights into the pathogenesis of tumors. However, the characteristics of chimeric genes are rarely studied. Here, we used weighted co-expression network analysis to investigate the biological roles and underlying mechanisms of chimeric genes. Download the pig transcriptome data, we screened chimeric genes and parental genes from 688 sequences and 153 samples, predict their domains, and analyze their associations. We constructed a co-expression network of chimeric genes in pigs and conducted Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis on the generated modules using DAVID to identify key networks and modules related to chimeric genes. Our findings showed that most of the protein domains of chimeric genes were derived from fused pre-genes. Chimeric genes were enriched in modules involved in the negative regulation of cell proliferation and protein localization to centrosomes. In addition, the chimeric genes were related to the growth factor-β superfamily, which regulates cell growth and differentiation. Furthermore, in helper T cells, chimeric genes regulate the specific recognition of T cell receptors, implying that chimeric genes play a key role in the regulation pathway of T cells. Chimeric genes can produce new domains, and some chimeric genes are a key role involved in pathway-related function. Most chimeric genes show binding activity. Domains of chimeric genes are derived from several combinations of parent genes. Chimeric genes play a key role in the regulation of several cellular pathways. Our findings may provide new directions to explore the roles of chimeric genes in tumors. The online version contains supplementary material available at 10.1186/s12957-021-02248-9.
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DOI：
10.3390/molecules23112798
发表时间：
2018-10-28
期刊：
Molecules (Basel, Switzerland)
影响因子：
--
作者：
Nguyen TH;Barr FG
通讯作者：
Barr FG
WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
影响因子：
14.9
作者：
Kodama Y;Shumway M;Leinonen R;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
DOI：
10.1093/bioinformatics/bts251
发表时间：
2012-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Jiao X;Sherman BT;Huang da W;Stephens R;Baseler MW;Lane HC;Lempicki RA
通讯作者：
Lempicki RA
影响因子：
3.5
作者：
Babteen, Nouf Abubakr;Fawzy, Manal S.;Elshazli, Rami M.
通讯作者：
Elshazli, Rami M.