Table 1.

Groups of Commonly Affected Pathway Maps in All 5 Differentiated Cell Lines (Based on Enrichment Analysis)

	Significance score [−log10(P value)]
Pathway map title	E12	E14	E15	E16	H9
Development
Development_transcription regulation of granulocyte development	4.14	1.39	3.53	1.46	3.48
Development_FGF-family signaling	3.87	2.23	4.39	1.86	6.78
Development_WNT signaling pathway. Part 2	2.74	4.25	7.64	4.46	5.93
Development_A2B receptor: action via G-protein alpha s	2.20	3.30	1.36	2.14	2.24
Development_delta- and kappa-type opioid receptors signaling via beta-arrestin	2.18	1.47	3.64	1.40	2.70
Development_PDGF signaling via STATs and NF-kB	1.67	4.61	2.35	1.46	3.48
Development_PACAP signaling in neural cells	1.39	4.43	3.79	3.54	1.69
Cytoskeleton remodeling and cell adhesion
Cytoskeleton remodeling_Neurofilaments	3.85	2.53	2.04	5.24	1.34
Cytoskeleton remodeling_Keratin filaments	2.95	2.73	4.92	3.09	2.42
Cell adhesion_endothelial cell contacts by junctional mechanisms	2.82	2.43	5.41	1.83	2.33
Cell adhesion_gap junctions	2.53	4.92	5.33	4.51	2.48
Cytoskeleton remodeling_TGF, WNT and cytoskeletal remodeling	2.39	5.17	7.48	3.73	6.41
Cell adhesion_ECM remodeling	2.12	4.35	1.60	3.85	3.57
Cell adhesion_tight junctions	1.50	3.38	5.66	2.41	3.61

Fourteen out of 23 pathway maps, statistically significantly perturbed in all 5 cell lines, belong to 3 general biological processes: development, cell adhesion, and cytoskeleton rearrangement. These maps were used as a source for composition of process-specific lists of genes with expression changes.

FGF, fibroblast growth factor; PDGF, platelet-derived growth factor; NF-kB, nuclear factor kappa B; TGF, transforming growth factor; ECM, extracellular matrix; WNT, wingless signaling; STAT, signal transducers and activators of transcription; PACAP, pituitary adenylate cyclase-activating polypeptide.