I was analysing public RNA-Seq datasets from GEO for arriving at the most affected pathways /GO terms using the edgeR program. My objective was to determine whether Ca signalling pathway had a considerable effect in the corresponding phenotype. I did a DE analysis with edgeR and arrived at result in which the Ca signalling pathway was one among the top (topKEGG) hundred pathways :
(No.80) Pathway N Up Down P.Up P.Down
path:hsa04020 Calcium signaling pathway 79 8 5 3.534894e-02 3.626250e-01 (at 2hr)
(No.72) Pathway N Up Down P.Up P.Down
path:hsa04020 Calcium signaling pathway 79 14 12 1.795998e-02 3.278448e-01 (at 4hr)
What can I conclude on this pathway regarding its effect ? Thanks in advance.