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
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.