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Table 1 Selected genes in key functional categories differentially expressed in biofilm compared to planktonic cells (both cultured in 4.5 mM [Ca2+]). Genes were selected based on fold change and their functional relevance

From: Transcriptome analysis of the fish pathogen Flavobacterium columnare in biofilm suggests calcium role in pathogenesis

Functional group RefSeq Product Fold change (log2) FDR (adjusted p value)
EPS/LPS biosynthesis
  WP_060381967.1 1,4-polygalactosaminidase 1.72 1.1E-19
WP_060381836.1 UDP-N-acetylmuramate--alanine ligase 1.24 4.1E-05
WP_060381978.1 SAM-dependent methyltransferase 1.04 3.8E-07
WP_060382475.1 Glycosyltransferase − 1.99 9.3E-03
Amino acid metabolism
  WP_060383852.1 Branched-chain amino acid aminotransferase −1.53 3.52E-16
WP_060382313.1 Anthranilate synthase −1.35 2.71E-10
WP_060382314.1 Anthranilate phosphoribosyltransferase −1.03 1.18E-06
WP_060382792.1 Glycyl aminopeptidase M61 1.11 2.2E-11
WP_060382658.1 Von 25illebrand factore type protein 1.54 5.8E-10
T9SS
  WP_060383582.1 T9SS C-terminal target domain-containing protein −1.53 3.52E-16
WP_060383402.1 T9SS C-terminal target domain-containing protein −1.13 3.07E-05
Nutrient limitation
  WP_060381920.1 Abortive phage infection protein 1.17 5.0E-08
WP_060383199.1 Ribosome inactivating protein 1.30 9.27E-10
WP_060381977.1 Protein-tryosine-phosphatase 1.04 1.39E-09
WP_060382448.1 DNA starvation protect protein under stressful or poor nutriention conditions 2.08 8.3E-23
Regulatory functions
  WP_060382614.1 AraC family transcriptional regulator 1.71 2.9E-11
WP_060381931.1 Transcriptional regulator 1.31 5.4E-08
WP_060381980.1 ArsR family iron regulation transcriptional regulator 1.54 4.7E-4
Oxidative stress response
  WP_060381974.1 Catalase 2.16 8.71E-10
WP_060381975.1 Alkyl hydroperoxide reductase 1.50 8.29E-15
WP_060382235.1 Cytochrome c peroxidase 1.41 1.31E-10
WP_014164670.1 Thiol reductase thioredoxin 1.03 2.35E-09
Respiratory metabolism
  WP_060381919.1 O-succinylbenzoic acid CoA ligase 1.11 7.3E-03
WP_060382480.1 Cytochrome C oxidase subunit III −2.12 7.45E-06
WP_060382479.1 Cytochrome c oxidase accessory protein CcoG −2.03 2.9E-06
WP_060382481.1 Cytochrome C oxidase subunit IV −1.74 2.3E-05
WP_060382478.1 Cytochrome C oxidase Cbb3 −1.74 1.94E-03
WP_060381577.1 Cytochrome c oxidase subunit I − 1.50 1.7E-02
WP_060381570.1 Cytochrome C −1.39 3.7E-04
WP_060381576.1 Cytochrome C oxidase subunit II −1.39 2.6E-02
WP_060381561.1 NADH dehydrogenase −1.27 6.5E-03
WP_060381560.1 NADH oxidoreductase (quinone) subunit F −1.18 6.1E-03
WP_060381566.1 NADH-quinone oxidoreductase subunit L −1.07 1.7E-03
WP_060381562.1 NADH:ubiquinone oxidoreductase subunit H −1.06 1.1E-02
WP_014164161.1 NADH-quinone oxidoreductase subunit I −1.00 9.1E-03