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Table 1 Ranked list of the most significant genes / COGs associated with greater biofilm growth at 22C than 37C using Scoary and Pyseer

From: Biofilm associated genotypes of multiple antibiotic resistant Pseudomonas aeruginosa

SCOARY
  COG / Gene Function Presence OR Ben p Example (isolate_gene position)
1 group_8321 Methyltransferase 68 6.389 0.018 WH-SGI-V-07050_00375
2 group_15072 Hypothetical 80 5.044 0.018 WH-SGI-V-07050_00461
3 group_1519 SAM-dependent methyltransferase 79 4.932 0.018 WH-SGI-V-07050_00374
4 group_15041 Integrating conjugative element protein 75 5.251 0.018 WH-SGI-V-07050_00387
5 group_11043 (arsC_1) Arsenate reductase (glutaredoxin) 78 4.823 0.018 WH-SGI-V-07050_00379
6 acr3 ACR3 family arsenite efflux transporter 78 4.823 0.018 WH-SGI-V-07050_00380
7 arsC_2 Arsenate reductase 78 4.823 0.018 WH-SGI-V-07050_00381
8 group_11046 ArsR family transcriptional regulator 78 4.823 0.018 WH-SGI-V-07050_00382
9 group_2314 Hypothetical 71 4.823 0.018 WH-SGI-V-07050_00373
10 arsH_1 Arsenical resistance protein 78 4.823 0.018 WH-SGI-V-07050_00378
11 ydfG NADP-dependent 3-hydroxy acid dehydrogenase 73 5.015 0.018 WH-SGI-V-07050_00440
12 group_15062 TetR/AcrR family transcriptional regulator 73 5.015 0.018 WH-SGI-V-07050_00441
13 group_11053 Integrating conjugative element relaxase, PFGI-1 class 77 4.715 0.018 WH-SGI-V-07050_00417
14 qorB Quinone oxidoreductase 77 4.715 0.018 WH-SGI-V-07050_00419
15 group_832 Hypothetical 77 4.715 0.018 WH-SGI-V-07050_00384
16 group_11042 Hypothetical 63 5.658 0.018 WH-SGI-V-07050_00376
17 group_15038 Integrating conjugative element protein pill, pfgi-1 76 4.608 0.018 WH-SGI-V-07050_00383
18 group_15039 TIGR03759 family integrating conjugative element protein 76 4.608 0.018 WH-SGI-V-07050_00385
19 group_15040 Transglycosylase SLT domain-containing protein 76 4.608 0.018 WH-SGI-V-07050_00386
20 group_11058 MgtC/SapB family protein 84 4.203 0.018 WH-SGI-V-07050_00439
PYSEER
  COG / Gene Function Presence Beta lrt p Example
1 group_8321 Methyltransferase 68 1.9200 0.0001 WH-SGI-V-07050_00375
2 group_15072 Hypothetical 80 1.6800 0.0001 WH-SGI-V-07050_00461
3 group_15041 Integrating conjugative element protein 75 1.6500 0.0002 WH-SGI-V-07050_00387
4 group_11114 Hypothetical 140 1.5000 0.0002 WH-SGI-V-07050_02801
5 group_1519 SAM-dependent methyltransferase 79 1.5700 0.0003 WH-SGI-V-07050_00374
6 group_3009 4-alpha-glucanotransferase 72 1.3700 0.0003 WH-SGI-V-07051_05729
7 clsA Major cardiolipin synthase ClsA 42 1.6900 0.0003 WH-SGI-V-07066_05171
8 ydfG NADP-dependent 3-hydroxy acid dehydrogenase 73 1.6200 0.0003 WH-SGI-V-07050_00440
9 group_15062 TetR/AcrR family transcriptional regulator 73 1.6200 0.0003 WH-SGI-V-07050_00441
10 group_11043 (arsC_1) Arsenate reductase (glutaredoxin) 78 1.5500 0.0003 WH-SGI-V-07050_00379
11 acr3 ACR3 family arsenite efflux transporter 78 1.5500 0.0003 WH-SGI-V-07050_00380
12 arsC_2 Arsenate reductase 78 1.5500 0.0003 WH-SGI-V-07050_00381
13 group_11046 ArsR family transcriptional regulator 78 1.5500 0.0003 WH-SGI-V-07050_00382
14 arsH_1 Arsenical resistance protein 78 1.5500 0.0003 WH-SGI-V-07050_00378
15 fliC Flagellin 109 1.2400 0.0004 WH-SGI-V-07064_05796
16 group_5435 Alpha/beta fold hydrolase 101 -1.1300 0.0004 WH-SGI-V-07049_05847
17 group_5843 Hypothetical 35 1.8200 0.0004 WH-SGI-V-07066_05167
18 group_2314 Hypothetical 71 1.5400 0.0004 WH-SGI-V-07050_00373
19 group_832 Hypothetical 77 1.5100 0.0004 WH-SGI-V-07050_00384
20 group_11053 Integrating conjugative element relaxase, PFGI-1 class 77 1.5000 0.0005 WH-SGI-V-07050_00417
  1. Presence = number of isolates (of 280) gene is present in. OR = Odds ratio and Ben p = Benjamini-Hochberg corrected p value for Scoary
  2. Beta = slope of regression and lrt p = likelihood ratio test p value using Pyseer. Genes in bold are present in both lists