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Table 3 edgeR results for HOMINGS probes abundant in ≥5 samples: WS microcosms vs. Plaque

From: Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries

HOMINGS taxon probea logFCb adjPValuec Abundance >1%d
Streptococcus_Genus_probe −2.99 1 9
Neisseria_Genus_probe 8.76 0.38 8
Rothia_Genus_probe 4.20 6.52E-03* 6
Granulicatella_adiacens_&_paradiacens −2.89 1 6
Haemophilus_parainfluenzae 2.15 1 6
Rothia_aeria 6.30 1 6
Streptococcus_gordonii_&_sanguinis −3.10 1 6
Veillonella_dispar −2.68 1 6
Fusobacterium_Genus_probe 2.10 1 6
Veillonella_Genus_probe −2.67 1 6
Corynebacterium_durum 8.51 <0.00E-163* 5
Lautropia_mirabilis 9.33 1.56E-09* 5
Abiotrophia_defectiva 4.93 5.36E-04* 5
Gemella_haemolysans 4.16 3.15E-03* 5
Rothia_dentocariosa 3.64 1 5
  1. aFormatted as per HOMINGS output
  2. bLog fold-change WS:P
  3. c p values adjusted using the Benjamini-Hochberg procedure, controlling the FDR at 5 %; an adjusted p value of 1 reflects rounding by Excel of values >0.999; asterisk indicates FDR ≤ 5 %
  4. dNumber of plaque samples in which reads for a probe were ≥1 % (as a percent of total reads)