Table 2.

Developmental, function and pathway analyses of 125 cotton fiber genes (Set 1) identified by expression profiling and double feature selection analysis highlighting the top represented GO pathways.

Cluster (genes)	Pima pattern	TM1 pattern	Top pathway (P value)	Top GO (P value)
1 (13)	Slightly up in SCW	Highly up in SCW	Reductive carboxylase cycle (0.013)	Response to biotic stimulus (0.02)
2 (34)	Down in SCW	Slightly up in the overlapped transition from PCW to SCW	Stilbene, cumarine and lignin biosynthesis (0)	Purine nucleotide binding (0.025)
3 (43)	Up in both PCW and SCW	Down in both PCW and SCW	Starch and Sucrose metabolism (0.03)	Sucrose metabolism (0.02)
4 (28)	Up in PCW and down in SCW	Up in both PCW and SCW	VEGF signaling pathway (0.02)	Serine-type peptidase activity (0.0003)
5 (7)	Down in the transition from PCW to SCW and up in SCW	Up in the PCW and down in the transition from PCW to SCW	Phenylalanine metabolism (0.004)	Transferase activity (0.01)