number of genes for co-expression network

Question

[Edalat]

Hi, I did differential expression by DEseq2 for some coding and lncoding RNAseq data,this is my summery result of DEseq2 by adjusted p-value < 0.1:

for lncoding:

out of 26998 with nonzero total read count

adjusted p-value < 0.1

LFC > 0 (up) : 10, 0.037%

LFC < 0 (down) : 13, 0.048%

outliers [1] : 241, 0.89%

low counts [2] : 11375, 42%

(mean count < 1)

and for coding:

out of 19933 with nonzero total read count

adjusted p-value < 0.1

LFC > 0 (up) : 335, 1.7%

LFC < 0 (down) : 300, 1.5%

outliers [1] : 289, 1.4%

low counts [2] : 6012, 30%

(mean count < 61)

as you see I have 23 genes for lncoding ad 635 genes for coding after filtering,this number of genes is OK for making co-expression network?

Answer 1

[shunyip]

You can draw a co-expression network with just two genes. If you do not set a correlation threshold, you will have a network with 2 nodes and 1 edge.

Since you have 658 genes, which will give you a maximum of around 200k edges, you can try out different thresholds to decrease the number of edges. I suggest that you should try out different thresholds to see if your network is fine. Whether it is OK or not depends on your data and your experiment.

I hope this helps.