Significant genes in RNA-seq

Question

[faqrulhasan10225]

Hello, i am new in this field. My professor has done RNA seq for prostrate cancer cell line before and after drug treatment and processed all data by some one else because she is not expert of RNA seq analysis. data shows different expression levels for many genes in two conditions. All data is organised in a excel. There are all data like fold changes, p value, q- value. some of genes are indicated also significant which q value less then 0.05. . She asked me to find potential target genes. Please tell me what is the meaning of significant genes. How can i find potential target genes.

Thank you in advance.

Answer 1

[Satyajeet Khare]

Genes that show significant change in expression. Based on q-value (generally <0.05) and the fold change (generally more than 2, increase or decrease). In your case you should can also take into the consideration the drug and shortlist genes more important to the treatment. Such as specific pathways.