Entering edit mode
3.5 years ago
ngarber
•
0
Hi all, I need some help analyzing RNA-seq data which has a list of differentially expressed genes. All expressed genes have values reported as FPKM. I need to predict the master transcription factor(s) that are driving the shift in transcriptome between the two conditions in my RNA-seq experiment. Help?
I've been trying to use Tetramer in Cytoscape for this, but every time I import the data, it says that it can't parse it and gives an error. I thought I formatted it correctly... 3 columns, A=gene name, B=FPKM in condition 1, C=FPKM in condition 2.
This is completely new for me. Any help is appreciated!
What is your organism? Can you give an example of gene name?
I've been treating it as human because almost all the genes are homologous and most TFs are described in humans, but the species is technically Capra hircus, the common goat. The samples are dermal papilla stem cells from primary hair follicles (top coat) vs. secondary hair follicles (undercoat). I want to know which TFs are controlling the transcriptional shift between the two follicle types.
I mean database in Tetramer as far as i know is for human and mice so gene names should be strictily identical to those in the database! ( PS: just a thought, I am not an expert)