Table 1.

Pathway population

Cell lineage identification	Hedgehog	P53	WNT targets	WNT	Cell cycle	VEGFs	Embryonic stem cells	Stem cell signalling	Homeobox	Stem cell TF	EMT	Jak-STAT	Stem cells	Terminal diff marker	Notch sig	Epigen chrom remod fact	Notch targets	Total number of pathways
		+	+	+			+			+		+	+					7
			+	+				+			+				+			5
							+	+		+	+	+						5
+			+				+			+			+					5
+			+				+			+								4
+			+									+					+	4
		+			+							+			+			4
							+	+				+						3
	+							+		+								3
								+	+	+								3
							+			+								2
									+	+								2
					+			+										2
										+						+		2
		+			+													2
										+								1
							+											1
							+											1
3	1	3	5	2	3	0	8	6	2	10	2	5	2	0	2	1	1	56

A list of genes selected from the 1100 upregulated genes in naïve vs primed-state embryonic stem cellss. The genes are ranked in ascending order based on the number of scores in different pluripotent-related cell pathways. (+) indicates that the gene is associated with the pluripotency-related pathways listed. Grey highlights the top 10 genes based on their involvement in > 3 pluripotent-related pathways. Three of the 4 Yamanaka factors fall in this list and are marked in bold with*. (Adapted from Mashayekhi et al[11]).