Table 4.

PAGE comparing biofilm versus planktonic phase^a

Biofilm	Gene set	Z score	Fold change	No. of genes	P value
Upregulated
Healthy	ko00195 photosynthesis	1.918	0.994	8	0.055
	ko00194 photosynthesis proteins	1.918	0.994	8	0.055
	ko02010 ABC transporters	1.761	0.269	92	0.078
	ko00630 glyoxylate and dicarboxylate metabolism	1.684	0.582	18	0.092
	ko01001 protein kinases	1.662	0.559	19	0.096
Pathogenic	ko02020 two-component system	3.328	0.619	77	0.001
	ko00940 phenyl propanoid biosynthesis	2.251	2.121	3	0.024
	ko02022 two-component system	2.124	0.517	45	0.034
	ko03000 transcription factors	2.040	0.375	79	0.041
	ko00910 nitrogen metabolism	2.038	0.513	42	0.042
	ko00591 linoleic acid metabolism	1.991	2.297	2	0.047
	ko00363 bisphenol A degradation	1.991	2.297	2	0.047
	ko00633 trinitrotoluene degradation	1.920	1.567	4	0.055
	ko02060 PTS	1.890	0.465	44	0.059
Downregulated
Healthy	ko00520 amino sugar and nucleotide sugar metabolism	−3.663	−0.849	40	0
	ko00010 glycolysis/gluconeogenesis	−4.072	−1.039	33	0
	ko03440 homologous recombination	−3.178	−1.042	20	0.001
	ko00980 metabolism of xenobiotics by cytochrome P450	−3.287	−3.407	2	0.001
	ko02060 PTS	−3.479	−0.787	42	0.001
	ko00982 drug metabolism-cytochrome P450	−3.139	−4.601	1	0.002
	ko00604 glycosphingolipid biosynthesis-ganglio series	−2.933	−4.299	1	0.003
	ko00531 glycosaminoglycan degradation	−2.933	−4.299	1	0.003
	ko00641 3-chloroacrylic acid degradation	−2.994	−2.194	4	0.003
	ko00500 starch and sucrose metabolism	−2.812	−0.765	29	0.005
	ko00511 other glycan degradation	−2.84	−1.574	7	0.005
	ko00071 fatty acid metabolism	−2.759	−1.43	8	0.006
	ko03030 DNA replication	−2.704	−0.991	16	0.007
	ko00624 1- and 2-methyl naphthalene degradation	−2.594	−1.437	7	0.009
	ko00061 fatty acid biosynthesis	−2.531	−1.071	12	0.011
	ko00550 peptidoglycan biosynthesis	−2.439	−0.688	27	0.015
	ko00740 riboflavin metabolism	−2.347	−1.216	8	0.019
Biofilm	ko03110 chaperones and folding catalysts	−2.311	−0.619	30	0.021
	ko00281 geraniol degradation	−2.315	−1.959	3	0.021
	ko00650 butanoate metabolism	−2.222	−0.627	27	0.026
	ko03018 RNA degradation	−2.187	−0.857	14	0.029
	ko00903 limonene and pinene degradation	−2.155	−1.58	4	0.031
	ko00930 caprolactam degradation	−2.022	−2.964	1	0.043
	ko00830 retinol metabolism	−1.964	−2.036	2	0.049
	ko00240 pyrimidine metabolism	−1.931	−0.396	51	0.053
	ko00072 synthesis and degradation of ketone bodies	−1.814	−1.329	4	0.07
	ko03032 DNA replication proteins	−1.797	−0.466	32	0.072
	ko00051 fructose and mannose metabolism	−1.786	−0.449	34	0.074
	ko02040 flagellar assembly	−1.769	−2.593	1	0.077
	ko00970 aminoacyl-tRNA biosynthesis	−1.7	−0.455	30	0.089
	ko00900 terpenoid backbone biosynthesis	−1.689	−0.554	20	0.091
Pathogenic	ko00240 pyrimidine metabolism	−4.135	−0.91	55	0
	ko03012 translation factors	−4.708	−2.131	13	0
	ko03011 ribosome	−6.072	−1.349	54	0
	ko03010 ribosome	−6.072	−1.349	54	0
	ko00230 purine metabolism	−3.23	−0.613	74	0.001
	ko03020 RNA-polymerase	−3.014	−1.555	10	0.003
	ko00710 carbon fixation in photosynthetic organisms	−2.85	−0.992	22	0.004
	ko00523 polyketide sugar unit biosynthesis	−2.657	−2.168	4	0.008
	ko00970 aminoacyl-tRNA biosynthesis	−2.548	−0.747	31	0.011
	ko03430 mismatch repair	−2.558	−0.89	22	0.011
	ko03400 DNA repair and recombination proteins	−2.297	−0.402	87	0.022
	ko00520 amino sugar and nucleotide sugar metabolism	−2.299	−0.559	45	0.022
	ko01002 peptidases	−1.926	−0.39	65	0.054
	ko03018 RNA degradation	−1.879	−0.767	16	0.06
	ko00983 drug metabolism, other enzymes	−1.829	−0.944	10	0.067
	ko00521 streptomycin biosynthesis	−1.765	−1.018	8	0.078
	ko00740 riboflavin metabolism	−1.679	−0.913	9	0.093
	ko00790 folate biosynthesis	−1.661	−0.752	13	0.097

^aGene sets are based on the KEGG orthology. Results show gene sets that were significantly upregulated in the biofilm fraction in relation to the planktonic fraction. “ko” numbers shown in the table correspond to KEGG metabolic pathways.