Table 1.

Ontological Clusters Formed by Genes Commonly Upregulated in Induced Pluripotent Stem Cells, Oncogenic Foci

Ontological clusters of upregulated genes	P value
Carbohydrate catabolic process	9.92×10−04
Glucose metabolic process	2.08×10−03
Cellular carbohydrate catabolic process	2.44×10−03
Lysosome	2.73×10−03
Sphingolipid metabolic process	2.75×10−03
Lytic vacuole	2.81×10−03
Membrane lipid metabolic process	3.09×10−03
Organophosphate metabolic process	6.40×10−03
Glucose catabolic process	1.29×10−02
Monosaccharide metabolic process	2.20×10−02
Positive regulation of inflammatory response	2.12×10−02
Response to wounding	4.58×10−02
Histone core	1.07×10−05
Nucleosome core	1.82×10−05
Stem cell maintenance	2.92×10−03
Stem cell development	3.33×10−03
Sugar/inositol transporter	7.46×10−03
Monosaccharide biosynthetic process	7.83×10−03
Alcohol biosynthetic process	1.28×10−02
Glutathione metabolic process	3.98×10−02
Nicotinamide metabolic process	3.98×10−02
Embryonic organ development	4.17×10−02
Monosaccharide metabolic process	4.17×10−02

Genes common in iPS1 and iPS2 (in dark gray), OF (Myc, Myc^TA, Myc^TA+Klf4, and SV40, in light gray).

Bolded entries denote clusters shared between conditions that arise from specific genes that are not commonly regulated; i.e., overlapping clusters from non-overlapping genes.