Metabolic dysfunction associated kidney disease GWAS and gsMAP

Header Explanations:SNP: Single Nucleotide Polymorphism identifier (e.g., rsID).CHR: Chromosome number where the SNP is located.BP: Base pair position of the SNP on the chromosome.MAF: Minor Allele Frequency (frequency of the less common allele, 0–0.5).A2: Other allele (reference/non-effect allele).A1: Effect allele (allele for which the effect size is estimated).i: Index/iteration number (e.g., model or subgroup identifier).lhs: Left-hand side of the SEM equation (dependent variable, e.g., trait/factor).op: SEM operator (e.g., ~ = regression, =~ = latent measurement).rhs: Right-hand side of the SEM equation (independent variable, e.g., SNP).est: Regression coefficient estimate (effect size of SNP on lhs).se_c: Standard error of the coefficient estimate (est).Z_Estimate: Z-score for the estimate (est / se_c).Pval_Estimate: P-value for the estimate (significance of est).Q: Cochran’s Q statistic (measures heterogeneity of effects across subgroups/studies).Q_df: Degrees of freedom for the Q statistic.Q_pval: P-value for Cochran’s Q (significance of heterogeneity; <0.05 indicates significant heterogeneity).N_hat: Estimated effective sample size (total or weighted sample size used in analysis).

This folder contains gsMap output for the traits Atrial Fibrillation and Sick Sinus Syndrome on the MOSTA E16.5_E1S1 spatial transcriptomics sample. For each trait, there are three visualization subfolders: gsMap_plot/ (spatial maps showing where the trait-associated signal is enriched across the tissue section), GSS_plot/ (plots of Gene Specificity Score, GSS, illustrating where candidate genes are specifically expressed in space), and manhattan_plot/ (GWAS-style Manhattan/diagnostic plots summarizing genomic association signals). In addition, E16.5_E1S1.MOSTA_*_Gene_Diagnostic_Info.csv provides a gene-level diagnostic table (e.g., genes with their spatial annotation, summary GSS metrics such as median GSS, and correlation-style indicators linking spatial specificity to GWAS signal), while E16.5_E1S1.MOSTA_*_gsMap_Report.html is an integrated HTML report that brings together the key figures and summaries for quick interpretation and result review.

### 表头说明：
SNP：单核苷酸多态性（Single Nucleotide Polymorphism）标识符，例如rsID。
CHR：该SNP所在的染色体编号。
BP：该SNP在染色体上的碱基对位置。
MAF：次要等位基因频率（Minor Allele Frequency，即低频等位基因的频率，取值范围为0~0.5）。
A2：其他等位基因（参考/非效应等位基因）。
A1：效应等位基因（用于估算效应量的等位基因）。
i：索引/迭代编号，例如模型或亚组标识符。
lhs：结构方程模型（Structural Equation Model, SEM）方程左侧，即因变量，例如性状/因子。
op：SEM运算符，例如~代表回归关系，=~代表潜在测量关系。
rhs：SEM方程右侧，即自变量，例如SNP。
est：回归系数估计值，即SNP对lhs的效应量。
se_c：系数估计值的标准误，即est的标准误。
Z_Estimate：估计值的Z分数，计算公式为est / se_c。
Pval_Estimate：估计值的P值，用于检验est的统计学显著性。
Q：科克伦Q统计量，用于衡量亚组或研究间效应的异质性。
Q_df：Q统计量对应的自由度。
Q_pval：科克伦Q检验的P值，用于检验异质性的显著性；当P<0.05时，表示存在显著异质性。
N_hat：估算的有效样本量，即分析中使用的总样本量或加权样本量。

本文件夹包含针对心房颤动（Atrial Fibrillation）与病窦综合征（Sick Sinus Syndrome）两个性状，在MOSTA E16.5_E1S1空间转录组样本上的gsMap分析输出结果。
针对每个性状，均设有三个可视化子文件夹：
1. gsMap_plot/：空间分布图，用于展示性状关联信号在组织切片中的富集区域；
2. GSS_plot/：基因特异性得分（Gene Specificity Score, GSS）可视化图，用于展示候选基因的空间特异性表达区域；
3. manhattan_plot/：全基因组关联研究（Genome-Wide Association Study, GWAS）风格的曼哈顿图/诊断图，用于汇总基因组关联信号。
此外，文件E16.5_E1S1.MOSTA_*_Gene_Diagnostic_Info.csv为基因水平诊断表，其中包含基因的空间注释信息、GSS汇总指标（如GSS中位数）以及连接空间特异性与GWAS信号的相关性类指标；文件E16.5_E1S1.MOSTA_*_gsMap_Report.html为集成化HTML报告，整合了关键图表与汇总结果，便于快速解读与结果复核。