Table 2.

Gene Ontology classes differentially affected by SDK as assessed by Panther^a

	U133 (REF) (Number of genes)	SDK down (Number of genes)	Expected (Number of genes)	P-value
Biological process
mRNA transcription	1462	92	32.21	2.33E−20
mRNA transcription regulation	1205	80	26.55	6.16E−19
Nucleoside, nucleotide and nucleic acid metabolism	2607	122	57.44	6.12E−17
Developmental processes	1776	62	39.13	1.94E−04
Cell cycle control	354	19	7.8	4.08E−04
MAPKKK cascade	194	13	4.27	4.58E−04
Stress response	164	11	3.61	1.22E−03
Other developmental process	94	8	2.07	1.31E−03
Angiogenesis	31	4	0.68	5.23E−03
Cell proliferation and differentiation	621	24	13.68	6.20E−03
Oncogenesis	499	20	10.99	8.25E−03
Molecular function
Transcription factor	1602	102	35.3	4.04E−23
Nucleic acid binding	2121	90	46.73	5.85E−10
Zinc finger transcription factor	619	38	13.64	1.97E−08
Transcription cofactor	137	16	3.02	1.08E−07
Other transcription factor	341	24	7.51	9.02E−07
Nuclease	220	14	4.85	4.66E−04
KRAB box transcription factor	423	20	9.32	1.35E−03
Chromatin/chromatin-binding protein	106	8	2.34	2.73E−03
Homeobox transcription factor	166	10	3.66	4.26E−03
Other zinc finger transcription factor	100	7	2.2	7.32E−03
Other signaling molecule	154	9	3.39	7.88E−03
HMG box transcription factor	36	4	0.79	8.73E−03
Pathway
Transcription regulation by bZIP transcription factor	42	5	0.93	2.59E−03
Interferon-gamma signaling pathway	32	4	0.71	5.83E−03
Wnt signaling pathway	289	13	6.37	1.30E−02
TGF-beta signaling pathway	105	6	2.31	3.02E−02
Hedgehog signaling pathway	33	3	0.73	3.74E−02
Apoptosis signaling pathway	123	6	2.71	5.69E−02

^aPanther analysis was done on the 460 transcripts with ≥2.5-fold decrease in expression after SDK treatment. Only classes found to be over-represented among SDK down-regulated genes and with lowest P-values are shown.