calculating down-regulated and upregulated genes from a set of values

Question

[biostudent]

if there is a set of values made from the ratio of protein abundance between two cell lines (determined from the sum of the peptide intensities) e.g. : gene - Gstm3 ; ratio intensity - 0.0486

What is the method for using a two-fold change in determining which genes have been up and down regulated? it would make sense if there were two sets of values of protein abundance for both cell lines, but this is slightly confusing...

[rpolicastro]

Can you explain your data and question in more detail? It's usually good to include some example data too.

[biostudent]

Hi, thank you for your reply.

So, the question is looking at proteomic profiles of two cancer cell lines which were compared using SILAC quantification. We're 'given the ratio of the protein abundance between each cell line determined from the sum of the peptide intensities. ≥2-fold change considered significant.' This is an example of some of the data:

Gene names - Ratio intensity cell line 1/cell line 2

QRSL1 - 0.0486

LAMB3 - 0.0540

BASP1 - 0.0658

AR - 0.0682

CCND1 - 0.0758

so essentially, we're meant to use a functional analysis software to input the data which describe the characteristics and functions of the proteins, and compare the two cell lines and the underlying disease mechanisms. The part i'm stuck on is how to 'use a 2 fold-change' on the ratio intensity between the cell lines ^ to determine which proteins are in higher or lower abundance compare to the other cell line, as I have no idea what the calculation for this is.

Hopefully, this was a little more detailed !

[rpolicastro]

If I understand correctly wouldn't it just be proteins with a ratio >2 or <-2 depending on what direction is interesting?