Table 6.

The functional groups whose genes were over-represented among top 100 genes, as identified by the joint model applied to the Lrp data set. The function code indicates which function group the genes belong to and the relationship among function groups in the tree structure. For example, function code 1.1.3 represents function “amino acids metabolism”; its parent node is function 1.1, “Carbon compound utilization ”; the function codes 1.1.3.2 and 1.1.3.7 are its child nodes, which are “L-serine degradation” and “Threonine catabolism” respectively.

Function names	Function code	P-values
Trehalose degradation	1.1.1.18	0.001897
Ribose degradation	1.1.1.22	0.006116
Amino acids metabolism	1.1.3	0.002218
L-serine degradation	1.1.3.2	0.000643
Threonine catabolism	1.1.3.7	0.000114
ATP proton motive force interconversion	1.3.8	0.002989
Serine biosynthesis	1.5.1.11	0.009022
Alanine biosynthesis	1.5.1.17	0.001897
Isoleucine biosynthesis	1.5.1.18	2.22E-07
Leucine biosynthesis	1.5.1.19	3.40E-05
Glycoprotein biosynthesis	1.6.11	0.001692
rRNA Information transfer	2.2.6	−2.09E-17
Nucleoproteins transfer	2.3.7	0.005848
periplasmic binding component transport	4.3.A.1.p	0.008304
F-ATPase Superfamily transport	4.3.A.2	0.001207
The PTS Galactitol (Gat) Family transport	4.4.A.5	0.006116
L-leucine transport	4.S.108	0.009022
H+ transport	4.S.82	0.000437
Adaptation to stress ( Osmotic Pressure)	5.5.1	0.000976
Adaptation to stress ( pH response)	5.5.4	1.06E-05
Transposon related	8.3	2.57E-09