Estrogen hormonal signalling genes

Question

[glady]

Hello,

I have downloaded gene expression data for NSCLC Tumor tissues from TCGA, it contains both Tumor_male and tumor_females.

How can I identify genes that are specifically regulated in NSCLC by estrogen hormonal signalling?

1) Will DESeq2 between the tumor_male and tumor_female give me the results? 2) or should I go for some statistical test like t-test or chi-squared test?

Thank you.

[ATpoint]

Definitely DESeq2, no homemade approaches. It will give you DEGs given that there are some. That will give you the gender effect for the tumor, which does not mean that this is necessarily due to hormone signaling, it is just the general gender effect which is more complex that signaling by estrogen alone, but the list could be used to perform functional enrichment analysis or compare it with lists of genes that are related to this signaling pathway.

[glady]

Thank you for your reply. By functional enrichment analysis, you mean performing a GO study or GSEA?

[glady]

And if I want to identify genes regulated in Males and Females, but also considering the differences between Tumor and Normal? Will a DESeq matrix with both conditions work for such an analysis?

dds = DESeqDataSetFromMatrix(data, colData, design = ~gender + condition)

[gender = male vs female, condition = tumor vs normal]