Systematic Analysis of Time-Series Gene Expression Data on Tumor Cell-Selective Apoptotic Responses to HDAC Inhibitors

Table 1

Pathway coherence changes by functional category.

Pathway category	Pathway count	Consistent high	Up	Down	Consistent low	(up versus down)
KEGG
Cellular processes	12	50	8.3	16.7	25	1
Environmental information processing	16	18.8	37.5	12.5	31.3	0.22
Genetic information processing	15	53.3	33.3	6.7	6.7	0.17
Human diseases	37	24.3	13.5	13.5	48.6	1
Metabolism	61	23	29.5	6.6	41	0.017
Organismal systems	35	11.4	28.6	5.7	54.3	0.02
BioCarta
Adhesion	11	27.3	9.1	0	63.6	1
Apoptosis	22	4.5	13.6	4.5	77.3	0.61
Cell activation	14	0	14.3	0	85.7	0.48
Cell cycle regulation	9	0	0	55.6	44.4	0.03
Cell signalling	106	3.8	16	6.6	73.6	0.11
Cytokinesis/chemokines	34	2.9	8.8	2.9	85.3	0.61
Developmental biology	11	9.1	18.2	0	81.8	0.48
Expression	15	0	33.3	20	46.7	0.68
Hematopoiesis	10	0	30	0	70	0.21
Immunology	39	0	10.3	0	89.7	0.12
Metabolism	2	50	0	0	50	1
Neuroscience	6	0	50	0	50	0.18