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Table 2 edgeR results for HOMINGS probes abundant in ≥5 samples: NS 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 1.64 1 9
Neisseria_Genus_probe 7.80 1 8
Rothia_Genus_probe 4.87 1.64E-04* 6
Fusobacterium_Genus_probe −5.44 1 6
Granulicatella_adiacens_&_paradiacens −2.07 1 6
Haemophilus_parainfluenzae −2.46 1 6
Streptococcus_gordonii_&_sanguinis −1.35 1 6
Veillonella_dispar −0.96 1 6
Veillonella_Genus_probe −0.35 1 6
Rothia_aeria 7.97 1 6
Lautropia_mirabilis 9.82 5.25E-05* 5
Abiotrophia_defectiva 2.28 2.87E-03* 5
Corynebacterium_durum 7.97 7.83E-22* 5
Rothia_dentocariosa 4.18 1 5
Gemella_haemolysans 0.63 1 5
  1. aFormatted as per HOMINGS output
  2. bLog fold-change NS: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)