Table 1 The core biofilm transcriptome.

From: Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype

Upregulated genes								Downregulated genes
Locus tag		Gene	Log 2 FC	Locus tag		Gene	Log 2 FC	Locus tag		Gene	Log 2 FC
PA14	PAO1	Gene		PA14	PAO1	Gene		PA14	PAO1	Gene
PA14_06090	PA0466		2.9	PA14_38850	PA1983	exaB	6.8	PA14_04650	PA0355	pfpI	−3.2
PA14_06180	PA0472	fiuI	2.5	PA14_38860	PA1982	exaA	5.8	PA14_06650	PA0509	nirN	−3.0
PA14_07355	PA0565		3.6	PA14_38880	PA1981		5.7	PA14_06660	PA0510	nirE	−3.3
PA14_09980	PA4167	dkgB	2.7	PA14_38900	PA1980	exaE	2.9	PA14_06670	PA0511	nirJ	−3.5
PA14_10170	PA4159	fepB	3.2	PA14_38910	PA1979	exaD	3.0	PA14_06680	PA0512	nirH	−3.2
PA14_10200	PA4156		2.8	PA14_38920	—		4.1	PA14_06690	PA0513	nirG	−2.9
PA14_10240	PA4152	acoC	2.8	PA14_38970	PA1976		2.9	PA14_06700	PA0514	nirL	−3.3
PA14_10250	PA4151	acoB	3.0	PA14_38990	PA1975		3.1	PA14_06710	PA0515	nirD	−3.3
PA14_10260	PA4150	acoA	3.1	PA14_39000	PA1974		4.9	PA14_06720	PA0516	nirF	−3.1
PA14_10270	PA4149	acoX	3.5	PA14_39050	PA1971	braZ	2.5	PA14_06730	PA0517	nirC	−3.9
PA14_10280	PA4148		3.6	PA14_39260	PA1952		2.7	PA14_06740	PA0518	nirM	−4.8
PA14_10400	—		3.2	PA14_39590	PA1927	metE	4.3	PA14_06750	PA0519	nirS	−4.9
PA14_10410	—		2.9	PA14_39720	PA1918		2.6	PA14_06770	PA0520	nirQ	−3.3
PA14_11070	PA4085	cupB2	2.7	PA14_39750	PA1916		2.7	PA14_06810	PA0523	norC	−5.9
PA14_19270	PA3467		2.7	PA14_39860	PA1907		2.5	PA14_06830	PA0524	norB	−4.5
PA14_20010	PA3408	hasR	3.3	PA14_39980	PA1898	qscR	2.6	PA14_06840	PA0525	norD	−4.4
PA14_20020	PA3407	hasAp	5.1	PA14_40040	PA1893		2.7	PA14_06860	PA0526		−3.9
PA14_20030	PA3406	hasD	3.1	PA14_40050	PA1892		2.7	PA14_09610	PA4200		−2.5
PA14_20040	PA3405	hasE	3.0	PA14_40060	PA1891		3.0	PA14_09660	PA4198		−2.6
PA14_20050	PA3404	hasF	2.7	PA14_40270	PA1873		2.8	PA14_16640	PA3691		−2.9
PA14_21530	PA3287		3.1	PA14_40520	PA1855		2.7	PA14_20180	PA3394	nosF	−2.8
PA14_22320	PA3237		4.0	PA14_41510	PA1783	nasA	2.8	PA14_20190	PA3393	nosD	−2.8
PA14_27370	PA2840	deaD	2.4	PA14_41520	PA1782	ppkB	2.6	PA14_20200	PA3392	nosZ	−4.8
PA14_28100	PA2783		2.6	PA14_41530	PA1781	nirB	2.7	PA14_20230	PA3391	nosR	−4.3
PA14_28360	—		2.7	PA14_44190	PA1569		2.8	PA14_29640	PA2664	fhp	−3.8
PA14_28620	PA2746		3.2	PA14_44520	PA1541	ydgF	3.3	PA14_29660	PA2662		−2.6
PA14_29350	PA2688	pfeA	2.6	PA14_44530	PA1540	ygdE	2.8	PA14_40850	PA1831	gpmA	−2.4
PA14_29480	PA2678	wzm	2.7	PA14_46850	PA1347		2.8	PA14_50520	PA1074	braC	−2.5
PA14_32080	PA2518	xylX	3.3	PA14_47380	PA1302	hxuC	2.6	PA14_52660	PA0899	aruB	−2.3
PA14_32100	PA2517	xylY	2.9	PA14_47390	PA1301		3.0	PA14_52670	PA0898	astD	−2.2
PA14_33250	PA2427		4.4	PA14_47400	PA1300		2.8	PA14_52690	PA0897	aruG	−3.0
PA14_33260	PA2426	pvdS	3.0	PA14_49690	PA1137		3.8	PA14_52720	PA0895	argD	−2.4
PA14_33270	PA2425	pvdG	4.0	PA14_50050	PA1108		2.6	PA14_56370	PA4336		−2.9
PA14_33280	PA2424	pvdL	3.8	PA14_51460	PA0993	cupC2	3.2	PA14_56780	PA4366	sodB	−2.6
PA14_33500	PA2413	pvdH	3.0	PA14_52960	PA0874		2.7	PA14_57020	PA4386	groES	−2.7
PA14_33510	PA2412		3.5	PA14_53300	PA0848		3.4	PA14_60570	PA4578		−2.9
PA14_33520	PA2411		3.7	PA14_55500	PA0680	hxcV	2.6	PA14_61650	PA4661	pagL	−2.7
PA14_33600	PA2403	fpvG	3.1	PA14_56770	PA4365		2.5	PA14_64480	PA4876	osmE	−2.7
PA14_33610	PA2400		2.9	PA14_57990	PA4467		3.1	PA14_64520	PA4880		−2.9
PA14_33690	PA2397	pvdE	3.3	PA14_58000	PA4468	sodM	3.1	PA14_69770	PA5285		−2.6
PA14_33710	PA2395	pvdO	3.0	PA14_58010	PA4469		3.5
PA14_33720	PA2394	pvdN	3.2	PA14_58030	PA4470	fumC	3.3
PA14_33730	PA2393		3.6	PA14_58040	PA4471		3.9
PA14_33810	PA2386	pvdA	4.5	PA14_60480	PA4570		4.1
PA14_33820	PA2385	pvdQ	3.3	PA14_68430	PA5180	fdhD	2.9
PA14_35430	PA2254	pvcA	2.7	PA14_68440	PA5181		2.5
PA14_35460	PA2252		2.9	PA2958.1	PA2958.1	rgsA	3.7
PA14_35980	—		2.9	PA3964-PA3965	PA3964-PA3965	P24	3.6
PA14_37380	PA2097		2.4	PA4704.1	PA4704.1	prrF1	3.3
PA14_38210	PA2034		2.6	PA4704.2	PA4704.2	prrF2	2.8
PA14_38220	PA2033		2.6	PA4704-PA4705	PA4704-PA4705	prrH	3.1
PA14_38310	PA2027		3.3

The analysis of differentially expressed genes between transcriptional profiles of 77 clinical P. aeruginosa isolates recorded under static biofilm (BF) and planktonic (PL) growth conditions resulted in the identification of 143 genes. 103 genes were significantly upregulated; 40 genes were significantly downregulated (threshold: log 2 fold change [log 2 FC] ≤ −2 and ≥2 with a false discovery rate of FDR < 0.05). Additional information about the identified genes (e.g., FDR values, gene products, and pseudoCAP) are available in Supplementary Data 1

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Table 1 The core biofilm transcriptome.

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