Table 1.

Model chronological profiles and enriched KEGG pathways within profiles

Model STEM Profiles		KEGG Pathway Enrichment Within Model STEM Chronological Profiles
Profile #	P Value	Annotated Genes, n	Pathway ID	Definition - Mus musculus (mouse)	Fisher P Value	Enrichment Score (-log10 P value)
1	0.00	174	mmu04141	protein processing in endoplasmic reticulum	9.58E−14	13.02
			mmu03060	protein export	4.32E−06	5.36
			mmu04910	insulin signaling pathway	2.47E−05	4.61
			mmu04130	SNARE interactions in vesicular transport	4.04E−05	4.39
2	0.00	96	mmu00190	oxidative phosphorylation	6.79E−05	4.17
3	3.50E−266	44	mmu04060	cytokine-cytokine receptor interaction	4.41E−05	4.36
			mmu04115	p53 signaling pathway	0.0160	1.80
4	5.30E−218	170	mmu04972	pancreatic secretion	2.60E−09	8.59
			mmu04911	insulin secretion	9.23E−08	7.03
			mmu04080	neuroactive ligand-receptor interaction	2.69E−05	4.57
	3.20E−210	127	mmu03030	DNA replication	2.08E−08	7.68
			mmu03440	homologous recombination	1.85E−05	4.73
			mmu03410	base excision repair	0.0010	3.01
6	4.50E−180	76	mmu01040	biosynthesis of unsaturated fatty acids	0.0012	2.94
			mmu01212	fatty acid metabolism	0.0057	2.24
7	3.00E−121	59	mmu00532	glycosaminoglycan biosynthesis	0.0094	2.03
			mmu00620	pyruvate metabolism	0.0149	1.83
8	7.40E−75	20	mmu00310	lysine degradation	0.0030	2.53
9	3.80E−70	40	mmu00020	citrate cycle (TCA cycle)	0.0053	2.28
			mmu04151	PI3K-Akt signaling pathway	0.0392	1.41
10	7.60E−70	82	mmu03020	RNA polymerase	3.23E−05	4.49
			mmu03050	proteasome	2.91E−03	2.54
			mmu04310	Wnt signaling pathway	1.34E−02	1.87
11	4.80E−47	75	mmu04015	Rap1 signaling pathway	6.44E−05	4.19
			mmu04014	Ras signaling pathway	0.0145	1.84
			mmu04350	TGF-beta signaling pathway	0.0490	1.31
12	2.90E−21	32	mmu04015	Rap1 signaling pathway	0.0090	2.05
			mmu00520	amino sugar and nucleotide sugar metabolism	0.0439	1.36
13	4.20E−17	84	mmu04660	T cell receptor signaling pathway	1.61E−09	8.79
			mmu04210	apoptosis	9.11E−07	6.04
14	7.20E−09	14	mmu00514	other types of O-glycan biosynthesis	0.0085	2.07
15	1.80E−08	12	mmu04915	estrogen signaling pathway	0.0180	1.74
16	4.10E−08	133	mmu04064	NF-kappa B signaling pathway	2.28E−08	7.64
			mmu04060	cytokine-cytokine receptor interaction	2.66E−07	6.58
			mmu04668	TNF signaling pathway	1.45E−05	4.84
17	3.00E−06	56	mmu04142	lysosome	0.0024	2.62
			mmu04330	Notch signaling pathway	0.0366	1.44
18	8.80E−05	44	mmu00190	oxidative phosphorylation	0.0009	3.04
19	0.01	110	mmu04662	B cell receptor signaling pathway	0.0002	3.72

Left: table depicts 19 distinct significant time-dependent model profiles (numbered 1–19) obtained by short time-series expression miner (STEM) analysis with corresponding P values for statistically significant overenrichment of genes. Right: number of annotated genes belonging to each of the 19 chronological profiles significantly enriched for specific KEGG biological pathways depicted with their respective Fisher P values and enrichment scores.