Thy1-haSyn and WT RNA-seq WGCNA - Brain and colon consensus network (brain adjacency)

Gene expression profiling was performed on gut (colon) and brain (striatal) tissue from mice overexpressing human wild type α–synuclein (Thy1-haSyn) and wild-type (WT) mice aged 1 and 3 months using 3′ RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was performed in R. Genes on the X chromosome, which contains the transgene, were excluded. For colon samples, a signed network was constructed based on biweight midcorrelations with a soft power threshold of eight. The percent of outliers for biweight midcorrelations was restricted to 5%. Module detection used a cut height of 0.995, a minimum module size of 60, and a deep split level of 1. Highly correlated modules (>0.75) were merged. Analysis for striatum used the same parameters except for a soft threshold power of 12 and restriction of outliers for biweight midcorrelations to 1%.

This consensus network contains all nodes with module membership ≥ 0.6 in either network. Edge weights were derived from the adjacency matrix for the brain/striatum network.
Consensus, colon adjacency: Thy1-haSyn and WT RNA-seq WGCNA - Brain and colon consensus network (colon adjacency) (e87d7969-eb45-11eb-b666-0ac135e8bacf) (ndexbio.org)
Tissue-specific networks:Brain: Thy1-haSyn and WT Striatum RNA-seq WGCNA (a207e9d0-5233-11ec-b3be-0ac135e8bacf) (ndexbio.org)
Colon: Thy1-haSyn and WT Colon RNA-seq WGCNA (d72dcf6e-eb40-11eb-b666-0ac135e8bacf) (ndexbio.org)

Code is available at https://github.com/videlock/Thy1-haSyn-Gut-Brain

本数据集采用3′RNA测序技术，对过表达人野生型α-突触核蛋白（α-synuclein）的Thy1-haSyn小鼠，以及1月龄、3月龄野生型（Wild Type, WT）小鼠的肠道（结肠）组织与脑组织（纹状体）开展基因表达谱分析。
使用R语言完成加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis, WGCNA），并剔除了携带转基因的X染色体上的基因。
针对结肠样本，基于双权重中位相关（biweight midcorrelations）构建有符号共表达网络，软阈值幂（soft power threshold）设为8；双权重中位相关的异常值占比被限制为5%。模块检测阶段设置截断高度为0.995、最小模块尺寸为60、深度分割水平为1；相关性≥0.75的高度相关模块将被合并。
纹状体样本的分析采用完全一致的参数，仅将软阈值幂调整为12，且双权重中位相关的异常值占比限制为1%。
本共识网络包含所有在任一子网络中模块隶属度（module membership）≥0.6的节点，边权重来源于脑组织/纹状体网络的邻接矩阵。
共识网络（结肠邻接型）：Thy1-haSyn与WT RNA-seq WGCNA——脑与结肠共识网络（结肠邻接型）(e87d7969-eb45-11eb-b666-0ac135e8bacf) (ndexbio.org)
组织特异性网络：
脑：Thy1-haSyn与WT纹状体RNA-seq WGCNA (a207e9d0-5233-11ec-b3be-0ac135e8bacf) (ndexbio.org)
结肠：Thy1-haSyn与WT结肠RNA-seq WGCNA (d72dcf6e-eb40-11eb-b666-0ac135e8bacf) (ndexbio.org)
相关代码已开源，获取地址为https://github.com/videlock/Thy1-haSyn-Gut-Brain