please help me to be clear about the up and down regulated genes from cuffdiff

Question

[zizigolu]

Hi,

Supposing I have samples C1 and C2 evaluated by cuffdiff. from genes_exp.diff file I extracted 56 genes whose log2(fold-change) is negative and 122 genes whose log2(fold-change) is positive all statistically are significant.

This means 56 genes up regulated in sample C1 and 122 gene up regulated in sample C2????

Thank you

Answer 1

[iraun]

The genes_exp.diff file is a tab delimited file with the results of differential expression testing between samples (C1 and C2 in your case) for genes. The fold-change value is calculated using the following formula: log2(FPKMy/FPKMx), being x and y C1 and C2 in your case. So, the positive values in FC means upregulated genes for C2 sample in comparison with C1, and negative values are indicating a downregulated expression in C2 in comparison with C1. The FC is always a comparison between two conditions.

I hope to clarify things to you a little bit.

[zizigolu]

Thank you, completely clear

Sorry I am right if I only used the significant ones (yes in column 14)?

[iraun]

Glad to help :)