Table 2.

Cellular functions with genes changed in mitomycin-C-treated cells relative to neural stem cells

GO Type	GO Name	Number Changed	Number Measured	Number in GO	Adjusted P Value
Downregulated
C	Chromosome	65	311	340	<0.0001
P	DNA replication	39	134	138	<0.0001
P	Cell cycle	82	593	633	<0.0001
P	Cell division	45	239	249	<0.0001
C	Nucleus	182	3642	3941	<0.0001
P	DNA packaging	25	116	126	<0.0001
P	Chromosome organization and biogenesis	40	325	346	<0.0001
C	Protein-DNA complex	19	94	108	<0.0001
P	DNA repair	25	175	189	<0.0001
P	DNA geometric change	4	7	7	<0.0001
F	DNA clamp loader activity	3	4	4	<0.0001
P	Deoxyribonucleotide biosynthetic process	3	5	6	0.025
F	DNA helicase activity	5	16	17	<0.0001
P	DNA recombination	11	76	84	<0.0001
F	Single-stranded DNA binding	5	18	20	<0.0001
F	ATP binding	49	1143	1237	<0.0001
P	Mitochondrial DNA metabolic process	4	17	18	0.047
C	Spindle	6	36	40	<0.0001
P	Microtubule-based movement	9	76	79	<0.0001
F	DNA-directed DNA polymerase activity	5	27	27	<0.0001
F	Microtubule motor activity	7	51	54	<0.0001
P	Nucleobase, nucleoside, nucleotide and nucleic acid transport	7	56	57	<0.0001
P	Plastid DNA metabolic process	5	32	34	0.025
P	Isoprenoid biosynthetic process	3	13	17	0.047
F	Damaged DNA binding	4	23	23	0.025
C	Microtubule associated complex	8	81	84	<0.0001
C	Microtubule	13	187	206	<0.0001
P	RNA splicing	12	170	183	<0.0001
P	Intracellular protein transport across a membrane	6	57	58	<0.0001
P	mRNA processing	13	218	234	<0.0001
F	ATP-dependent helicase activity	6	62	66	<0.0001
P	Microtubule cytoskeleton organization and biogenesis	6	68	75	0.025
P	Purine salvage	47	1717	1843	<0.0001
Upregulated
C	Extracellular region	90	1422	1562	<0.0001
F	Growth factor activity	18	135	149	<0.0001
P	Collagen catabolic process	5	16	16	<0.0001
P	Positive regulation of cell proliferation	19	191	208	<0.0001
F	Hexosaminidase activity	4	14	14	0.045
F	Hormone activity	11	104	111	<0.0001
P	Nucleosome assembly	9	87	94	0.045
C	Nucleosome	9	87	99	<0.0001
P	Positive regulation of lymphocyte activation	8	72	80	<0.0001
C	Lysosome	13	167	177	<0.0001
P	Regulation of lymphocyte activation	9	103	111	<0.0001
P	Antiapoptosis	7	71	74	<0.0001
P	Cell cycle arrest	5	43	46	<0.0001
P	Regulation of lymphocyte proliferation	6	59	63	0.045
P	Response to stress	38	931	1034	0.045
P	Negative regulation of programmed cell death	11	175	188	<0.0001
P	Growth	17	339	368	0.045

Abbreviations: GO, Gene Ontology; P, biological process; C, cellular component; F, molecular function.