Thy1-haSyn and WT RNA-seq WGCNA - Gut-Proteolysis (darkmagenta) module

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 selected nodes with module membership ≥ 0.6. Edge weights were derived from the adjacency matrix.
Full networks:
Colon: Thy1-haSyn and WT Colon RNA-seq WGCNA (d72dcf6e-eb40-11eb-b666-0ac135e8bacf) (ndexbio.org)

Brain: Thy1-haSyn and WT Striatum RNA-seq WGCNA (a207e9d0-5233-11ec-b3be-0ac135e8bacf) (ndexbio.org)

Consensus networks

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，对过表达人野生型α-突触核蛋白（Thy1-haSyn）的转基因小鼠与野生型（wild-type, WT）1月龄及3月龄小鼠的肠道（结肠）和脑组织（纹状体）样本开展基因表达谱分析。采用R语言进行加权基因共表达网络分析（Weighted gene co-expression network analysis, WGCNA），并剔除了携带外源转基因的X染色体上的所有基因。针对结肠样本，基于双权重中相关系数构建有符号共表达网络，软阈值幂值设置为8，双权重中相关系数的异常值占比被限制为5%。模块检测环节采用的切割高度为0.995，最小模块大小为60，深度分割水平为1；相关性系数大于0.75的模块将进行合并。纹状体样本的分析采用完全一致的参数，仅将软阈值幂值调整为12，且异常值占比限制为1%。

本网络选取模块隶属度≥0.6的节点进行分析，边权重由邻接矩阵推导得到。

完整网络如下：
结肠样本网络：Thy1-haSyn与WT小鼠结肠RNA-seq WGCNA (d72dcf6e-eb40-11eb-b666-0ac135e8bacf) (ndexbio.org)
脑组织（纹状体）样本网络：Thy1-haSyn与WT小鼠纹状体RNA-seq WGCNA (a207e9d0-5233-11eb-b3be-0ac135e8bacf) (ndexbio.org)

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

相关代码已公开于https://github.com/videlock/Thy1-haSyn-Gut-Brain