Canonical pathway analysis (GeneGo maps) as evaluated acknowledged function-specific genes significantly present within the network [5]. Acknowledgments This study was partially supported by the United States Department of Agriculture Research Specific Cooperative agreement No. 58-6408-1-603-04. Appendix ...
WGCNA 是一种基于基因表达数据的系统生物学方法,通过构建基因共表达网络,识别高度协同表达的基因模块(Module,并探索这些模块与表型(如疾病、生理特征)之间的关联。其核心思想是:“共表达的基因可能在功能上相关” 。 基因共表达网络 :以基因表达数据为基础,计算基因间的表达相关性(如皮尔逊相关系数),构建无尺度网络(S...
基因功能分析——Gene functional analysis KEGG 数据库简介 KEGG(Kyoto Encyclopedia of Genes and Genomes,京都基因与基因组百科全书)是一个数据库资源,用于从分子水平的信息,了解生物系统(如细胞、生物体和生态系统)的高层次功能和效用。 KEGG 核心数据库—— KEGG pathway简介 KEGG pathway是以KEGG Orthology (KO)...
PAGODA全称pathway and gene set overdispersion analysis,pagoda是2016年在nature methods发表的一个分析单细胞测序的方法,主要特点是在已知的重要信号通路基础上对细胞进行分类,以提高统计效力并揭示可能的功能性解释。同时RNA速率推断细胞演化velocyto是基于pagoda,因此有必要学一下pagoda。 生信编程日常 2020/04/09 1.7K1...
Differential network analysis The proposed framework for conducting a differential network analysis is summarized in the following steps, with details given in the proceeding sections. 1. Given a pathway G, compute the estimated association networks, \({\hat{S}}^{1}\) and \({\hat{S}}^{2...
We then replicated these findings in the Diabetes Genetics Replication and Meta-analysis (DIAGRAM) study. Many of the pathways identified have been proposed as important candidate pathways for T2D, including the calcium signaling pathway, the PPAR signaling pathway, and TGF-β signaling. Importantly,...
Network visualization of enriched pathways (GO/KEGG)24in the gene signature was performed by ClueGO analysis. (A) BP vs. P and (B) P vs. AP. Full size image The ‘protein processing in endoplasmic reticulum’ is the most important common pathway between associated modules and the DEGs. ...
Network-based Pathway Analysis"(GANPA).Through analysis of several microarray datasets,including the p53 dataset,asthma dataset and three breast cancer datasets,we demonstrated that our approach is biologically reliable and reproducible,and therefore helpful for microarray data interpretation and hypothesis ...
According to the molecular functions and biological processes mentioned above, the most relevant gene network induced by TNFα was related to the immune response and immunological disease functions (additional file 7). Instead, the anisomycin gene network was related to the regulation of cell ...
Pathway Analysis is statistically linking observations on the molecular level to biological processes or pathways on the systems(i.e., organism, organ, tissue, cell) level. Traditionally, pathway analysis methods regard pathways as collections of single genes and treat all genes in a pathway as equ...