Table 2. IPA enrichment analysis of human orthologs for three types of delay relative to mouse/bovine transcripts.

Delay compared to human	Organism	Pathway (# Transcripts identified/# Transcripts in pathway)	P value
>0	Mouse	EIF2 Signaling (79/173)	7.94 × 10−18
		mTOR Signaling (71/183)	5.64 × 10−12
		Regulation of eIF4 and p70S6K Signaling (60/143)	5.72 × 10−11
	Bovine	Protein Ubiquitination Pathway (54/254)	6.28 × 10−09
		Amyloid Processing (19/50)	4.36 × 10−08
		Glucocorticoid Receptor Signaling (51/272)	1.03 × 10−06
0	Mouse	Role of Macrophages, Fibroblasts and Endothelial Cells in Rheumatoid Arthritis (196/286)	1.84 × 10−31
		Role of Osteoblasts, Osteoclasts and Chondrocytes in Rheumatoid Arthritis (149/213)	6.88 × 10−27
		Axonal Guidance Signaling (115/157)	1.29 × 10−22
	Bovine	Protein Kinase A Signaling (199/370)	7.11 × 10−16
		Thrombin Signaling (116/187)	1.44 × 10−15
		Acute Phase Response Signaling (106/168)	4.51 × 10−15
<0	Mouse	Ephrin Receptor Signaling (76/172)	8.39 × 10−13
		Molecular Mechanism of Cancer (128/359)	5.26 × 10−12
		B Cell Receptor Signaling (71/171)	1.54 × 10−10
	Bovine	EIF2 Signaling (91/173)	1.75 × 10−25
		Regulation of eIF4 (55/143)	3.48 × 10−09
		Protein Ubiquitination Pathway (83/254)	5.11 × 10−09
>0, 0, <0	Mouse,	EIF2 Signaling (32/173)	1.59 × 10−17
	Bovine	Regulation of eIF4 (21/143)	5.25 × 10−10
		Acetyl-CoA Biosynthesis I (Pyruvate Dehydrogenase Complex) (4/6)	8.71 × 10−06

The top three IPA enriched pathways are listed. Associated transcripts were analysed separately with respect to the delay: positive (negative) delay indicates that the mouse or bovine ortholog’s expression changes occurred prior to (after) the human expression changes. No delay indicates that all expression changes occurred simultaneously. P values were obtained from a right tailed Fisher’s Exact Test as implemented by IPA.