Differential expressed genes for GRN

Question

[marwwa11]

Hi biostars, please after doing the differnetial expression analysis between 2 conditions (cell type 1 vs cell type 2)using limma, I will have a list of significant genes. If I am interested to GRN in the cell 1 (the cell 2 is used just for the analysis,) so I must take only the genes up expressed in this cell or all the DEG genes? Sorry for this banal question. Thanks

Answer 1

[Kevin Blighe]

To avoid ambiguity, please don't use undefined acronyms. By 'GRN', I presume that you mean gene regulatory network? The information about up- and down-regulated genes are just as important as each other for a network analysis, i.e., cell-types can be equally defined as what is expressed as what is not expressed.

Kevin

[marwwa11]

Ok, thank you very much