Table 1.

Significantly perturbed pathways in PIK3CA H1047R samples found by TimeTP and comparison with other representative pathway tools (+: found, −: not found)

Pathway	Pathway name	DEG P-value	Path	Path P-value	Combined P-value	Sub-pathway		Pathway		References
						non-TS	TS	non-TS	TS
						DEAP	TimeClip	SPIA	TRAP
hsa04012	ErbB signaling pathway	0.000	Path1	0.000	0.000	−	−	−	−	Hynes and Lane (2005)
hsa04810	Regulation of actin cytoskelet…	0.000	Path1	0.001	0.000	−	−	−	−	Jiménez et al. (2000)
			Path2	0.005	0.000
hsa04520	Adherens junction	0.000	Path1	0.020	0.000	−	−	−	−	Berglund et al. (2013)
hsa04310	Wnt signaling pathway	0.001	Path1	0.021	0.000	−	+	−	−	Essers et al. (2005), Perry et al. (2011), Vadlakonda et al. (2013)
hsa04510	Focal adhesion	0.000	Path1	0.024	0.000	−	+	+	+
hsa04068	FoxO signaling pathway	0.004	Path1	0.027	0.000	−	−	−	−	Zhang et al. (2011)
hsa04666	Fc gamma R-mediated phagocytos…	0.003	Path1	0.019	0.001	−	−	−	−	Zhang et al. (2010)
hsa04151	PI3K-Akt signaling pathway	0.032	Path1	0.005	0.001	−	+	−	+	Kiselev et al. (2015)
hsa04114	Oocyte meiosis	0.032	Path1	0.020	0.005	−	−	−	−	Coticchia et al. (2009)
hsa04921	Oxytocin signaling pathway	0.032	Path1	0.023	0.006	−	−	−	+	Coticchia et al. (2009)
TS: time-series.

Pathways with DEG P-value and sub-path P-value below 0.05 are shown.