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构建方法说明/RNA-seq sex-check APP description.md

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+# RNA-seq sex-check APP
+
+## 构建方法
+
+1. Identify sex-specific genes based on GTEx dataset
+   - In specific tissue type: female vs male: |logFC| >1 and t-test p value <0.05 
+   - Identified as a sex-specific genes across all 22 tissue types
+
+2. Identify method and cutoff using 70% of TCGA dataset
+   - Pairwise comparison: ExpMale-specific vs ExpFemale-specific 
+   - Cutoff: n of comparisons >0: male, otherwise female 
+3. Validate method based on external and independent datasets
+   - 30% of TCGA dataset
+   - lung cancer dataset
+   - TNBC dataset
+
+
+
+## 结果
+
+### Sex-specific genes in GTEx
+
+- Nineteen male-specific and two female-specific genes are identified. 
+- Five male-specific and two female-specific genes are selected for further analysis.
+
+![1568020621372](C:\Users\YY\AppData\Roaming\Typora\typora-user-images\1568020621372.png)
+
+
+
+### 训练集结果
+
+基于训练集，10次Male vs Female specific基因比较中，8次或以上Male > Female specific gene，则为Male，反之则为Female
+
+### 测试集结果
+
+都不错。
+
+| Dataset        | TP   | FP   | FN   | TN   | Precision | Sensitivity | Specificity | F1    |
+| -------------- | ---- | ---- | ---- | ---- | --------- | ----------- | ----------- | ----- |
+| TrainData_TCGA | 3748 | 48   | 27   | 4419 | 0.987     | 0.993       | 0.989       | 0.990 |
+| TestData_TCGA  | 1626 | 23   | 11   | 1873 | 0.986     | 0.993       | 0.988       | 0.990 |
+| TestData_LC    | 153  | 3    | 0    | 241  | 0.981     | 1.000       | 0.988       | 0.990 |
+| TestData TNBC  | 0    | 0    | 0    | 448  | NA        | NA          | 1           | NA    |
+
+
+
+### 结论
+
+建立了预测性别的方法：对每个待测样本，提取5个男性特有基因（RPS4Y1, DDX3Y, EIF1AY, KDM5D, TXLNGY）和2个女性特有基因（XIST, TSIX) 的表达水平，进行男性特有基因与女性特有基因的两两比较，共10次比较中，若超过(>=)8次比较中，男性特有基因表达水平高于女性特有基因表达水平，则为男性，反之则为女性。