使用基因表达数据推断基因网络与应用程序
1Department of Applied Mathematics, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City, 40227, Taiwan.
Heliyon
|March 7, 2024
概括
我们开发了NetARD和GNCE方法,从基因表达数据中推断基因网络 (GN),提高识别关键枢纽基因和生物过程的准确性. 这些方法提高了对复杂基因相互作用的理解.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 系统生物学 系统生物学
背景情况:
- 基因网络 (GNs) 使用图表建模基因相互作用,通常具有稀疏结构和关键的枢纽基因.
- 从大规模的基因表达数据中推断准确的GN是计算上具有挑战性的.
研究的目的:
- 提出NetARD,一种使用自动相关性确定 (ARD) 进行部分相关性估计的新方法,以推断带有枢纽基因的GN.
- 将NetARD集成到GN共同表达扩展 (GNCE) 中,以推断使用预定义的GN作为枢纽的共同表达基因网络.
- 应用这些方法来识别生物相关的基因相互作用和通路.
主要方法:
- 网ARD:使用ARD进行部分相关性估计,以推断基因网络.
- GNCE:将NetARD与预定义的基因集 (例如转录因子) 集成,以扩展基因网络.
- 验证:对模拟和in silico GNs,大肠杆菌转录因子数据和结直肠癌RNA-seq数据进行测试.
主要成果:
- 从模拟和in silico数据中推断基因网络,NetARD的性能优于现有的方法.
- 通过使用大肠杆菌转录因子数据验证,GNCE成功扩展了已知的基因网络.
- 对结直肠癌数据的分析确定了与癌症进展有关的显著生物过程.
结论:
- NetARD提供了一种有效的方法来推断基因网络,并从基因表达数据中识别枢纽基因.
- 通过利用先前的生物知识,GNCE增强了基因网络推断.
- 这些方法在识别与疾病相关的途径和生物过程方面具有实际应用.
关键词:
在 ARD ARD 里面.癌症 癌症 癌症 癌症共同表达是一种共同表达.基因表达 基因表达 基因表达哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈哈推理推理是指一个推理.网络 网络 网络 网络 网络 网络部分相关性 部分相关性更多相关视频
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