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

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.

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。