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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)