| 引用本文: | 方宏源,昝乡镇,沈良忠,刘文斌.一种基于基因拓扑重要性的通路识别方法[J].生物信息学,2017,15(4):214-220. |
| FANG Hongyuan,ZAN Xiangzhen,SHEN Liangzhong,LIU Wenbin.A pathway analysis method based on the topological importance of genes[J].Chinese Journal of Bioinformatics,2017,15(4):214-220. |
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| 摘要: |
| 癌症相关通路的识别是认识癌症发生发展过程机制的生物学基础。已有的通路识别方法很少考虑基因在通路中的拓扑重要性。重叠基因降权(PADOG)方法在基因集分析(GSA)方法的基础上融入了基因特异性的影响,提高了癌症相关通路的识别性能。为进一步提高癌症相关通路的识别性能,首先统计了KEGG通路数据集中基因出度的分布情况,根据基因出度的大小定义了基因的重要性。最后将基因的特异性和重要性融合在一起,提出了一种基于基因重要性和特异性的通路分析方法PAGIS。在结肠癌、肺癌和胰腺癌3个数据集上的实验结果表明,PAGIS方法比PADOG能够提高很多癌症相关的排名,从而提高癌症相关通路的识别效果。 |
| 关键词: 癌症 基因表达谱 通路分析 基因特异性 基因重要性 |
| DOI：10.3969/j.issn.1672-5565.201702003 |
| 分类号:TP311.13; R730.5 |
| 文献标识码:A |
| 基金项目:国家自然科学基金(7,8,61573017)；浙江省自然科学基金(lq17c060001)；温州大学研究生创新基金(3162014037). |
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| A pathway analysis method based on the topological importance of genes |
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FANG Hongyuan1, ZAN Xiangzhen2, SHEN Liangzhong2, LIU Wenbin1
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(1.College of Physics and Electronic Information Engineering, Wenzhou University, Wenzhou 325035, Zhejiang, China; 2. College of Information Engineering, Wenzhou Business College, Wenzhou 325035, Zhejiang, China)
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| Abstract: |
| Identifying cancer-related pathways is important for understanding the underling mechanisms of the development of cancers. However, current pathway analysis methods are lack of the consideration of topology characteristics of genes in the pathways. Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) considered the specificity of genes based on the GSA method to improve its performance. In order to improve the performance of identifying cancer-related pathways, we first studied the out-degree distribution of genes in the KEGG pathway database. Then we defined the importance of genes based on their out-degree. Finally we proposed a pathway analysis based on the important and specificity of genes (PAGIS). Analysis results from the colorectal cancer datasets showed that our improved method could identify more cancer related pathways than PADOG. |
| Key words: Cancer Gene expression profile Pathway analysis Gene specificity Gene importance |
