Genome-wide investigation of light and carbon signaling interactions in Arabidopsis

Table 3 Primary functional categories whose genes show over-representation or under-representation in InterAct class 000

Primary funcat	Total number of genes in a funcat assigned an InterAct class	Number of genes in InterAct class 000	Significance of class 000 in funcat	Number of other significant InterAct classes in funcat
Total	1,898	440	N/A	N/A
Metabolism*	274	45	-S	2
Protein fate (modification, folding, destination)	149	22	-S	2
Protein synthesis	106	12	-S	5
Energy	81	3	-S	1
Cell rescue, defense and virulence	76	10	-S	1
Unclassified proteins	632	167	+S	2
Transcription	135	45	+S	3
Cellular communication/signal transduction	130	43	+S	2
Cell cycle and DNA processing	49	17	+S	1
Cell fate	47	16	NS	2
Subcellular localization	387	76	NS	1
Transport facilitation	122	30	NS	1
Control of cellular organization	61	10	NS	2
Development (systemic)	51	17	NS	1
Systemic regulation of/interaction with environment	39	10	NS	2
Regulation of/interaction with cellular environment	25	4	NS	3
Protein activity regulation	14	4	NS	1
Organ differentiation	4	0	NS	1

The table indicates those funcats that are responding to light and/or carbon (for example, under-represented in InterAct class 000). -S or +S means that the genes in a particular functional category are significantly (p < 0.05) under-represented or over-represented in InterAct class 000, respectively. N/A, not applicable. Numbers in bold type are statistically significant; NS, non-significant. * The funcat that is the focus of this paper.

ISSN: 1474-760X