Thy1-haSyn and WT Brain (striatum) RNA-seq WGCNA

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 network contains all nodes with module membership ≥ 0.6. Edge weights were derived from the adjacency matrix.

Colon Network: Thy1-haSyn and WT Colon RNA-seq WGCNA (d72dcf6e-eb40-11eb-b666-0ac135e8bacf) (ndexbio.org)

Consensus network

Colon adjacency: Thy1-haSyn and WT RNA-seq WGCNA - Brain and colon consensus network (colon adjacency) (e87d7969-eb45-11eb-b666-0ac135e8bacf) (ndexbio.org)

Striatum adjacency: Thy1-haSyn and WT RNA-seq WGCNA - Brain and colon consensus network (brain adjacency) (d01c04e6-eb45-11eb-b666-0ac135e8bacf) (ndexbio.org)

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

本研究采用3'端RNA测序技术，对过表达人类野生型α-突触核蛋白（Thy1-haSyn）的小鼠以及1月龄、3月龄的野生型（WT）小鼠的肠道（结肠）和脑组织（纹状体）进行了基因表达谱分析。
研究通过R语言完成加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis，WGCNA），并排除了携带转基因的X染色体上的所有基因。
针对结肠样本，研究基于双权重中间相关（Biweight Midcorrelation）构建有符号网络，软阈值幂次阈值设为8，双权重中间相关的异常值占比被限制为5%。模块检测参数设置为：切割高度0.995、最小模块规模60、深度分裂水平1；将相关性高于0.75的高度相似模块进行合并。
纹状体组织的分析采用完全一致的参数，仅软阈值幂次设为12，且双权重中间相关的异常值占比限制为1%。
本网络包含所有模块隶属度≥0.6的节点，边权重由邻接矩阵推导得到。

结肠网络：Thy1-haSyn与WT小鼠结肠RNA-seq WGCNA（d72dcf6e-eb40-11eb-b666-0ac135e8bacf）（ndexbio.org）

共识网络
结肠邻接矩阵：Thy1-haSyn与WT小鼠RNA-seq WGCNA - 脑与结肠共识网络（结肠邻接矩阵）（e87d7969-eb45-11eb-b666-0ac135e8bacf）（ndexbio.org）
纹状体邻接矩阵：Thy1-haSyn与WT小鼠RNA-seq WGCNA - 脑与结肠共识网络（脑邻接矩阵）（d01c04e6-eb45-11eb-b666-0ac135e8bacf）（ndexbio.org）

相关代码可在https://github.com/videlock/Thy1-haSyn-Gut-Brain获取。