code depends on metagenomeSeq and other libraries that must be installed via either Bioconductor or CRAN. Some libraries that were used in this analysis were removed from CRAN e.g. ('biom'). You may need install these libraries (e.g. using devtools::install_github) manually to run these scripts.
data which will be used by the scripts is located in the data/ folder
alpha diversity
soource('figure_1a.R')
script generates
results/figure_1a_class.pdf
which was modified manually (using pvalues from supplementary table 2) to create part a of ms/version_september_17/figure1.pdf
triplot
soource('figure_1b.R')
script generates
results/figure_1b_triplot.pdf
which was modified to create part b of ms/version_september_17/figure1.pdf
alpha diversity
soource('figure_1c.R')
script generates
results/figure_1c_chao1.pdf- test statistics gets printed to screen:
Tukey multiple comparisons of means
95% family-wise confidence level
Fit: aov(formula = value ~ type, data = df.adiv)
$type
diff lwr upr p adj
control-AIH -0.2994906 -1.252769 0.65378825 0.7308472
others-AIH -0.8918631 -1.806463 0.02273673 0.0574292
others-control -0.5923725 -1.463349 0.27860441 0.2384276
which was modified manually to create part c of ms/version_september_17/figure1.pdf
PCOA
soource('figure_2a.R')
script generates
results/figure_2a_print.pdfresults/figure_2a_label.pdf
which was modified manually to create part a of ms/version_september_17/figure2.pdf
PCOA contrained by cohort
soource('figure_2b.R')
script generates
results/figure_2b_constrained_by_cohort_print.pdfresults/figure_2b_constrained_by_cohort_label.pdf
which was modified manually to create part b of ms/version_september_17/figure2.pdf
PCOA contrained by cohort
soource('figure_2c.R')
script generates
results/figure_2b_constrained_by_liver_print.pdfresults/figure_2b_constrained_by_liver.pdfresults/figure_2b_constrained_by_liver_label.pdf
which was modified manually to create part c of ms/version_september_17/figure2.pdf
analysis on OTU level
soource('figure_3.R')
script generates
results/figure_3_triplot.pdfresults/figure_3_aih_db.csvresults/figure_3_control_db.csvresults/figure_3_healthy_db.csv
which was modified manually to create ms/version_september_17/figure3.pdf
soource('figure_s1.R')
script generates
results/figure_s1a_observed.pdfresults/figure_s1b_shannon.pdf
which was modified manually to create part c of ms/version_september_17/figure_s3.pdf
soource('figure_s2.R')
script generates
results/figure_s2.pdf
which was modified manually to create part c of ms/version_september_17/figure_s2.pdf
soource('figure_s3.R')
script generates
results/figure_s3.pdf
which was modified manually to create part c of ms/version_september_17/figure_s3.pdf
statistical significance between groups: P = 0.00311
Df Sum Sq Mean Sq F value Pr(>F)
marker 3 920347 306782 5.212 0.00311 **
Residuals 54 3178690 58865
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
detailed statistics:
Tukey multiple comparisons of means
95% family-wise confidence level
Fit: aov(formula = chao1 ~ marker, data = alpha)
$marker
diff lwr upr p adj
keine_hepatopathie-hepatop_ohne_veraenderung 152.38325 -146.9897 451.75620 0.5361788
mit_fibrose-hepatop_ohne_veraenderung -67.77229 -394.1865 258.64188 0.9460486
mit_zirrhose-hepatop_ohne_veraenderung -140.15217 -437.8757 157.57134 0.5995773
mit_fibrose-keine_hepatopathie -220.15553 -461.5826 21.27157 0.0858399
mit_zirrhose-keine_hepatopathie -292.53541 -493.4835 -91.58736 0.0016946
mit_zirrhose-mit_fibrose -72.37988 -311.7586 166.99883 0.8533967
correlation coefficients will be printed to screen (for chao1, shannon, observed)
shannon
> printCorrelationCoef(chao1)
control
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "others"), ]$adiv and df.adiv[which(df.adiv$type == "others"), ]$ifap
t = -1.2159, df = 19, p-value = 0.2389
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.6275839 0.1843826
sample estimates:
cor
-0.2686908
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "others"), ]$adiv and df.adiv[which(df.adiv$type == "others"), ]$lbp
t = 0.47462, df = 19, p-value = 0.6405
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.3392953 0.5158291
sample estimates:
cor
0.1082462
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "others"), ]$adiv and df.adiv[which(df.adiv$type == "others"), ]$sCD14
t = -0.96352, df = 19, p-value = 0.3474
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.5923340 0.2380273
sample estimates:
cor
-0.2158375
healthy
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "control"), ]$adiv and df.adiv[which(df.adiv$type == "control"), ]$ifap
t = -0.21226, df = 10, p-value = 0.8362
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.6171537 0.5271918
sample estimates:
cor
-0.06697288
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "control"), ]$adiv and df.adiv[which(df.adiv$type == "control"), ]$lbp
t = -0.72758, df = 10, p-value = 0.4836
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.7071303 0.4013207
sample estimates:
cor
-0.2242239
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "control"), ]$adiv and df.adiv[which(df.adiv$type == "control"), ]$sCD14
t = -0.14956, df = 9, p-value = 0.8844
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.6308246 0.5670197
sample estimates:
cor
-0.04979144
AIH
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "AIH"), ]$adiv and df.adiv[which(df.adiv$type == "AIH"), ]$ifap
t = 0.58046, df = 14, p-value = 0.5708
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.3705645 0.6031700
sample estimates:
cor
0.1533008
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "AIH"), ]$adiv and df.adiv[which(df.adiv$type == "AIH"), ]$lbp
t = 0.70243, df = 14, p-value = 0.4939
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.3425250 0.6232134
sample estimates:
cor
0.1845082
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "AIH"), ]$adiv and df.adiv[which(df.adiv$type == "AIH"), ]$sCD14
t = -2.4767, df = 14, p-value = 0.02664
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.82259702 -0.07744908
sample estimates:
cor
-0.5519635
all
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "AIH" | df.adiv$type == "control" | and df.adiv[which(df.adiv$type == "AIH" | df.adiv$type == "control" | df.adiv$type == "others"), ]$adiv and df.adiv$type == "others"), ]$ifap
t = -2.2723, df = 47, p-value = 0.02769
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.54738273 -0.03665839
sample estimates:
cor
-0.3146119
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "AIH" | df.adiv$type == "control" | and df.adiv[which(df.adiv$type == "AIH" | df.adiv$type == "control" | df.adiv$type == "others"), ]$adiv and df.adiv$type == "others"), ]$lbp
t = -0.54859, df = 47, p-value = 0.5859
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.3530432 0.2060530
sample estimates:
cor
-0.07976532
Pearson's product-moment correlation
data: df.adiv[which(df.adiv$type == "AIH" | df.adiv$type == "control" | and df.adiv[which(df.adiv$type == "AIH" | df.adiv$type == "control" | df.adiv$type == "others"), ]$adiv and df.adiv$type == "others"), ]$sCD14
t = -3.8275, df = 46, p-value = 0.0003892
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
-0.6805680 -0.2409882
sample estimates:
cor
-0.4914704
statistics on class level
soource('table_s2.R')
script generates
results/table_s2_class_aih_vs_control.tsvtable_s2_class_aih_vs_helathy.tsvtable_s2_class_healthy_vs_control.tsv
which was modified manually to create ms/version_september_17/Table_S2.xlsx
| Class* | logFC | t | P value | FDR | B | sig. Level |
|---|---|---|---|---|---|---|
| RF3 | 1.47 | 3.45 | 0.003716 | 0.027254 | -1.92 | * |
| Opitutae | 1.18 | 1.96 | 0.083799 | 0.307263 | -4.45 | n.s. |
| Deferribacteres | 1.03 | 1.55 | 0.142350 | 0.377765 | -4.80 | n.s. |
| [Lentisphaeria] | 0.72 | 0.87 | 0.402788 | 0.579287 | -5.98 | n.s. |
| Erysipelotrichi | 0.37 | 1.10 | 0.277168 | 0.435550 | -6.44 | n.s. |
| Clostridia | 0.33 | 2.32 | 0.024737 | 0.136056 | -4.48 | n.s. |
| 4C0d-2 | 0.15 | 0.30 | 0.769840 | 0.865654 | -6.62 | n.s. |
| Mollicutes | 0.11 | 0.13 | 0.899250 | 0.905493 | -6.62 | n.s. |
| Deltaproteobacteria | -0.05 | -0.12 | 0.905493 | 0.905493 | -6.85 | n.s. |
| Bacilli | -0.09 | -0.27 | 0.786958 | 0.865654 | -7.03 | n.s. |
| Bacteroidia | -0.11 | -0.57 | 0.572722 | 0.699994 | -6.90 | n.s. |
| Alphaproteobacteria | -0.18 | -0.81 | 0.421300 | 0.579287 | -6.73 | n.s. |
| Betaproteobacteria | -0.25 | -1.10 | 0.276335 | 0.435550 | -6.44 | n.s. |
| Verrucomicrobiae | -0.36 | -0.60 | 0.554026 | 0.699994 | -6.71 | n.s. |
| Coriobacteriia | -0.43 | -1.29 | 0.204429 | 0.408857 | -6.20 | n.s. |
| Flavobacteriia | -0.49 | -1.17 | 0.257856 | 0.435550 | -5.86 | n.s. |
| Chloroplast | -0.50 | -1.42 | 0.166344 | 0.377765 | -5.76 | n.s. |
| Actinobacteria | -0.62 | -1.45 | 0.154523 | 0.377765 | -6.02 | n.s. |
| Epsilonproteobacteria | -0.93 | -1.42 | 0.171711 | 0.377765 | -5.54 | n.s. |
| Gammaproteobacteria | -1.38 | -4.05 | 0.000203 | 0.002229 | 0.01 | * * |
| Deinococci | -1.87 | -2.07 | 0.073636 | 0.307263 | -4.22 | n.s. |
| Fusobacteriia | -2.33 | -6.53 | 0.000001 | 0.000022 | 5.67 | * * * |
| Class* | logFC | t | P value | FDR | B | sig. Level |
|---|---|---|---|---|---|---|
| Fusobacteriia | 1.67 | 3.39 | 0.0027 | 0.0314 | -1.57 | * |
| Gammaproteobacteria | 1.51 | 4.28 | 0.0001 | 0.0027 | 1.04 | * * |
| Synergistia | 0.76 | 0.81 | 0.4371 | 0.7733 | -5.16 | n.s. |
| Verrucomicrobiae | 0.44 | 0.83 | 0.4101 | 0.7733 | -6.00 | n.s. |
| Actinobacteria | 0.41 | 1.08 | 0.2876 | 0.7158 | -5.87 | n.s. |
| Bacteroidia | 0.29 | 1.39 | 0.1728 | 0.6025 | -5.50 | n.s. |
| Coriobacteriia | 0.29 | 1.03 | 0.3112 | 0.7158 | -5.91 | n.s. |
| Betaproteobacteria | 0.24 | 0.94 | 0.3523 | 0.7365 | -5.99 | n.s. |
| Erysipelotrichi | 0.23 | 0.72 | 0.4743 | 0.7791 | -6.18 | n.s. |
| RF3 | 0.21 | 0.41 | 0.6899 | 0.8755 | -5.71 | n.s. |
| Bacilli | 0.16 | 0.56 | 0.5804 | 0.8343 | -6.29 | n.s. |
| Deferribacteres | 0.14 | 0.28 | 0.7846 | 0.8755 | -5.90 | n.s. |
| 4C0d-2 | 0.13 | 0.26 | 0.7980 | 0.8755 | -6.06 | n.s. |
| Deinococci | 0.11 | 0.15 | 0.8809 | 0.9210 | -5.61 | n.s. |
| Chloroplast | 0.11 | 0.26 | 0.7993 | 0.8755 | -6.17 | n.s. |
| Epsilonproteobacteria | 0.05 | 0.08 | 0.9404 | 0.9404 | -5.98 | n.s. |
| Clostridia | -0.25 | -1.32 | 0.1937 | 0.6025 | -5.59 | n.s. |
| Flavobacteriia | -0.25 | -0.57 | 0.5737 | 0.8343 | -5.86 | n.s. |
| Mollicutes | -0.28 | -0.38 | 0.7050 | 0.8755 | -6.12 | n.s. |
| Alphaproteobacteria | -0.37 | -1.56 | 0.1264 | 0.5814 | -5.26 | n.s. |
| Deltaproteobacteria | -0.45 | -1.28 | 0.2096 | 0.6025 | -5.55 | n.s. |
| [Lentisphaeria] | -1.27 | -1.83 | 0.0861 | 0.4953 | -4.37 | n.s. |
| Opitutae | -1.52 | -1.99 | 0.0719 | 0.4953 | -4.05 | n.s. |
| Class* | logFC | t | P value | FDR | B | sig. Level |
|---|---|---|---|---|---|---|
| RF3 | 1.68 | 2.34 | 0.04 | 0.51 | -4.57 | n.s. |
| Deferribacteres | 1.17 | 0.85 | 0.42 | 0.84 | -4.60 | n.s. |
| Erysipelotrichi | 0.60 | 1.54 | 0.13 | 0.63 | -4.54 | n.s. |
| 4C0d-2 | 0.28 | 0.36 | 0.72 | 0.92 | -4.61 | n.s. |
| Bacteroidia | 0.18 | 0.93 | 0.36 | 0.84 | -4.60 | n.s. |
| Gammaproteobacteria | 0.14 | 0.37 | 0.71 | 0.92 | -4.63 | n.s. |
| Clostridia | 0.08 | 0.48 | 0.64 | 0.92 | -4.63 | n.s. |
| Verrucomicrobiae | 0.07 | 0.10 | 0.92 | 0.96 | -4.63 | n.s. |
| Bacilli | 0.07 | 0.17 | 0.86 | 0.94 | -4.64 | n.s. |
| Betaproteobacteria | 0.00 | -0.02 | 0.98 | 0.98 | -4.64 | n.s. |
| Coriobacteriia | -0.14 | -0.44 | 0.66 | 0.92 | -4.63 | n.s. |
| Mollicutes | -0.17 | -0.18 | 0.86 | 0.94 | -4.61 | n.s. |
| Actinobacteria | -0.21 | -0.53 | 0.60 | 0.92 | -4.63 | n.s. |
| Elusimicrobia | -0.28 | -0.19 | 0.86 | 0.94 | -4.60 | n.s. |
| Opitutae | -0.34 | -0.47 | 0.65 | 0.92 | -4.60 | n.s. |
| Chloroplast | -0.39 | -0.76 | 0.45 | 0.84 | -4.61 | n.s. |
| Deltaproteobacteria | -0.50 | -1.07 | 0.30 | 0.84 | -4.59 | n.s. |
| [Lentisphaeria] | -0.56 | -0.79 | 0.44 | 0.84 | -4.60 | n.s. |
| Alphaproteobacteria | -0.56 | -2.17 | 0.04 | 0.51 | -4.45 | n.s. |
| TM7-3 | -0.58 | -0.85 | 0.42 | 0.84 | -4.60 | n.s. |
| Fusobacteriia | -0.66 | -1.29 | 0.21 | 0.72 | -4.58 | n.s. |
| Flavobacteriia | -0.74 | -1.48 | 0.16 | 0.64 | -4.58 | n.s. |
| Epsilonproteobacteria | -0.88 | -1.69 | 0.10 | 0.63 | -4.55 | n.s. |
| Deinococci | -1.76 | -1.69 | 0.13 | 0.63 | -4.59 | n.s. |
statistics on family level
soource('table_s3.R')
script generates
results/table_s3_family_aih_vs_control.tsvtable_s3_family_aih_vs_helathy.tsvtable_s3_family_healthy_vs_control.tsv
which was modified manually to create ms/version_september_17/Table_S3.xlsx
| Family* | logFC | t | P value | FDR | B | sig. Level |
|---|---|---|---|---|---|---|
| Fusobacteriaceae | -2.23 | -5.37 | 0.00001 | 0.0004 | 3.65 | * * * |
| Prevotellaceae | -1.89 | -3.16 | 0.00265 | 0.0212 | -2.31 | * |
| Deinococcaceae | -1.87 | -1.81 | 0.09122 | 0.2128 | -4.44 | n.s. |
| Veillonellaceae | -1.79 | -4.70 | 0.00002 | 0.0005 | 2.35 | * * * |
| Enterococcaceae | -1.65 | -2.98 | 0.00647 | 0.0362 | -2.57 | * |
| Enterobacteriaceae | -1.64 | -3.45 | 0.00122 | 0.0114 | -1.52 | * |
| Pasteurellaceae | -1.52 | -3.70 | 0.00065 | 0.0090 | -0.82 | * * |
| Leuconostocaceae | -1.49 | -1.64 | 0.12009 | 0.2495 | -4.71 | n.s. |
| Micrococcaceae | -1.47 | -2.39 | 0.02366 | 0.0780 | -3.90 | n.s. |
| Staphylococcaceae | -1.41 | -2.61 | 0.01496 | 0.0573 | -3.35 | n.s. |
| Streptococcaceae | -1.36 | -3.11 | 0.00311 | 0.0218 | -2.46 | * |
| Campylobacteraceae | -1.34 | -1.79 | 0.08719 | 0.2123 | -4.78 | n.s. |
| Gemellaceae | -1.30 | -2.28 | 0.03212 | 0.0947 | -4.03 | n.s. |
| [Paraprevotellaceae] | -1.28 | -2.67 | 0.01156 | 0.0498 | -3.41 | * |
| Carnobacteriaceae | -1.21 | -3.48 | 0.00119 | 0.0114 | -1.44 | * |
| Moraxellaceae | -1.13 | -2.29 | 0.02858 | 0.0889 | -4.18 | n.s. |
| [Weeksellaceae] | -1.03 | -1.49 | 0.15262 | 0.2849 | -5.16 | n.s. |
| Rhodobacteraceae | -0.93 | -1.16 | 0.25988 | 0.4158 | -5.61 | n.s. |
| Corynebacteriaceae | -0.87 | -1.66 | 0.10904 | 0.2442 | -5.15 | n.s. |
| Sphingomonadaceae | -0.76 | -2.51 | 0.01535 | 0.0573 | -3.93 | n.s. |
| Eubacteriaceae | -0.73 | -1.21 | 0.24008 | 0.3954 | -5.57 | n.s. |
| Actinomycetaceae | -0.70 | -1.76 | 0.08416 | 0.2123 | -5.35 | n.s. |
| Comamonadaceae | -0.66 | -2.16 | 0.03542 | 0.0992 | -4.62 | n.s. |
| Peptococcaceae | -0.61 | -1.33 | 0.19561 | 0.3423 | -5.56 | n.s. |
| Lactobacillaceae | -0.43 | -0.90 | 0.37561 | 0.5535 | -6.41 | n.s. |
| Coriobacteriaceae | -0.43 | -1.25 | 0.21907 | 0.3717 | -6.13 | n.s. |
| Verrucomicrobiaceae | -0.36 | -0.62 | 0.53792 | 0.6148 | -6.57 | n.s. |
| Bifidobacteriaceae | -0.36 | -0.72 | 0.47494 | 0.5811 | -6.66 | n.s. |
| Caulobacteraceae | -0.32 | -0.69 | 0.49812 | 0.5811 | -6.38 | n.s. |
| Methylobacteriaceae | -0.31 | -0.36 | 0.72166 | 0.7924 | -6.06 | n.s. |
| Pseudomonadaceae | -0.29 | -0.69 | 0.49613 | 0.5811 | -6.46 | n.s. |
| Peptostreptococcaceae | -0.24 | -0.42 | 0.67333 | 0.7541 | -6.69 | n.s. |
| Alcaligenaceae | -0.23 | -0.69 | 0.49373 | 0.5811 | -6.62 | n.s. |
| Desulfovibrionaceae | -0.08 | -0.19 | 0.84964 | 0.8811 | -6.71 | n.s. |
| Oxalobacteraceae | -0.02 | -0.05 | 0.96040 | 0.9604 | -6.91 | n.s. |
| Neisseriaceae | 0.04 | 0.05 | 0.95947 | 0.9604 | -6.15 | n.s. |
| [Tissierellaceae] | 0.12 | 0.25 | 0.80721 | 0.8529 | -6.54 | n.s. |
| [Odoribacteraceae] | 0.13 | 0.30 | 0.76323 | 0.8219 | -6.80 | n.s. |
| [Mogibacteriaceae] | 0.23 | 0.75 | 0.45851 | 0.5811 | -6.62 | n.s. |
| Bacteroidaceae | 0.26 | 0.69 | 0.49086 | 0.5811 | -6.69 | n.s. |
| Clostridiaceae | 0.30 | 0.80 | 0.42928 | 0.5811 | -6.60 | n.s. |
| Erysipelotrichaceae | 0.37 | 1.07 | 0.29030 | 0.4394 | -6.34 | n.s. |
| Dehalobacteriaceae | 0.50 | 0.77 | 0.44726 | 0.5811 | -6.13 | n.s. |
| Bradyrhizobiaceae | 0.53 | 0.81 | 0.42790 | 0.5811 | -5.96 | n.s. |
| Porphyromonadaceae | 0.62 | 1.58 | 0.12030 | 0.2495 | -5.60 | n.s. |
| Victivallaceae | 0.72 | 0.88 | 0.39199 | 0.5629 | -5.86 | n.s. |
| Lachnospiraceae | 0.75 | 2.69 | 0.00958 | 0.0483 | -3.51 | * |
| Ruminococcaceae | 0.80 | 2.66 | 0.01036 | 0.0483 | -3.58 | * |
| S24-7 | 0.84 | 1.56 | 0.12653 | 0.2531 | -5.58 | n.s. |
| Turicibacteraceae | 0.88 | 1.48 | 0.14561 | 0.2812 | -5.67 | n.s. |
| Deferribacteraceae | 1.03 | 1.11 | 0.27826 | 0.4328 | -5.20 | n.s. |
| Rikenellaceae | 1.12 | 2.09 | 0.04174 | 0.1113 | -4.81 | n.s. |
| Christensenellaceae | 1.14 | 2.50 | 0.01643 | 0.0575 | -3.89 | n.s. |
| [Cerasicoccaceae] | 1.18 | 1.42 | 0.17454 | 0.3153 | -5.05 | n.s. |
| [Barnesiellaceae] | 1.46 | 3.02 | 0.00395 | 0.0246 | -2.68 | * |
| no match | 1.96 | 4.38 | 0.00006 | 0.0011 | 1.28 | * * |
| Family* | logFC | t | P value | FDR | B | sig. Level |
|---|---|---|---|---|---|---|
| Succinivibrionaceae | 1.98 | 1.02 | 0.33 | 0.62 | -4.75 | n.a. |
| Prevotellaceae | 1.95 | 3.38 | 0.00 | 0.07 | -1.19 | n.a. |
| Pasteurellaceae | 1.53 | 3.25 | 0.00 | 0.07 | -1.57 | n.a. |
| Dehalobacteriaceae | 1.30 | 2.10 | 0.05 | 0.34 | -3.80 | n.a. |
| Fusobacteriaceae | 1.25 | 2.53 | 0.02 | 0.25 | -3.11 | n.a. |
| Veillonellaceae | 1.08 | 2.90 | 0.01 | 0.10 | -2.35 | n.a. |
| Peptococcaceae | 0.79 | 1.58 | 0.13 | 0.49 | -4.48 | n.a. |
| Streptococcaceae | 0.77 | 2.07 | 0.05 | 0.34 | -4.07 | n.a. |
| Micrococcaceae | 0.64 | 1.09 | 0.29 | 0.62 | -5.11 | n.a. |
| Staphylococcaceae | 0.63 | 1.60 | 0.12 | 0.49 | -4.55 | n.a. |
| Moraxellaceae | 0.63 | 1.62 | 0.12 | 0.49 | -4.61 | n.a. |
| Pseudomonadaceae | 0.59 | 1.37 | 0.18 | 0.50 | -4.95 | n.a. |
| Carnobacteriaceae | 0.56 | 1.47 | 0.15 | 0.50 | -4.92 | n.a. |
| Campylobacteraceae | 0.54 | 0.69 | 0.50 | 0.75 | -5.25 | n.a. |
| [Paraprevotellaceae] | 0.51 | 0.95 | 0.35 | 0.62 | -5.45 | n.a. |
| Comamonadaceae | 0.50 | 1.31 | 0.20 | 0.50 | -5.17 | n.a. |
| Caulobacteraceae | 0.46 | 0.95 | 0.35 | 0.62 | -5.33 | n.a. |
| Enterobacteriaceae | 0.44 | 0.94 | 0.36 | 0.62 | -5.50 | n.a. |
| Verrucomicrobiaceae | 0.44 | 0.83 | 0.41 | 0.67 | -5.60 | n.a. |
| Sphingomonadaceae | 0.41 | 1.29 | 0.20 | 0.50 | -5.22 | n.a. |
| Peptostreptococcaceae | 0.37 | 0.66 | 0.51 | 0.75 | -5.67 | n.a. |
| Actinomycetaceae | 0.36 | 1.11 | 0.27 | 0.62 | -5.42 | n.a. |
| [Weeksellaceae] | 0.35 | 0.59 | 0.56 | 0.75 | -5.35 | n.a. |
| Gemellaceae | 0.30 | 0.62 | 0.54 | 0.75 | -5.40 | n.a. |
| Bifidobacteriaceae | 0.30 | 0.63 | 0.53 | 0.75 | -5.81 | n.a. |
| Coriobacteriaceae | 0.29 | 1.00 | 0.33 | 0.62 | -5.54 | n.a. |
| [Odoribacteraceae] | 0.23 | 0.51 | 0.61 | 0.75 | -5.89 | n.a. |
| Lactobacillaceae | 0.23 | 0.50 | 0.62 | 0.75 | -5.84 | n.a. |
| Erysipelotrichaceae | 0.23 | 0.71 | 0.48 | 0.75 | -5.78 | n.a. |
| Eubacteriaceae | 0.18 | 0.39 | 0.70 | 0.79 | -5.51 | n.a. |
| Deferribacteraceae | 0.14 | 0.27 | 0.79 | 0.86 | -5.51 | n.a. |
| Oxalobacteraceae | 0.12 | 0.34 | 0.73 | 0.81 | -5.93 | n.a. |
| Bacteroidaceae | 0.03 | 0.10 | 0.92 | 0.97 | -6.02 | n.a. |
| Alcaligenaceae | 0.02 | 0.05 | 0.96 | 1.00 | -6.00 | n.a. |
| Clostridiaceae | 0.00 | 0.00 | 1.00 | 1.00 | -6.03 | n.a. |
| Corynebacteriaceae | -0.01 | -0.01 | 0.99 | 1.00 | -5.59 | n.a. |
| Desulfovibrionaceae | -0.16 | -0.43 | 0.67 | 0.78 | -5.80 | n.a. |
| Christensenellaceae | -0.20 | -0.52 | 0.61 | 0.75 | -5.81 | n.a. |
| Rikenellaceae | -0.26 | -0.56 | 0.58 | 0.75 | -5.87 | n.a. |
| Porphyromonadaceae | -0.32 | -0.96 | 0.34 | 0.62 | -5.54 | n.a. |
| Turicibacteraceae | -0.33 | -0.55 | 0.59 | 0.75 | -5.79 | n.a. |
| [Mogibacteriaceae] | -0.35 | -1.10 | 0.28 | 0.62 | -5.42 | n.a. |
| Ruminococcaceae | -0.37 | -1.58 | 0.12 | 0.49 | -4.85 | n.a. |
| Lachnospiraceae | -0.39 | -1.84 | 0.07 | 0.48 | -4.46 | n.a. |
| Rhodobacteraceae | -0.39 | -0.46 | 0.65 | 0.77 | -5.21 | n.a. |
| Bradyrhizobiaceae | -0.55 | -0.89 | 0.39 | 0.65 | -5.14 | n.a. |
| S24-7 | -0.62 | -1.36 | 0.18 | 0.50 | -5.06 | n.a. |
| [Barnesiellaceae] | -0.72 | -1.29 | 0.20 | 0.50 | -5.24 | n.a. |
| [Tissierellaceae] | -0.94 | -1.45 | 0.16 | 0.50 | -4.64 | n.a. |
| -1.00 | -2.25 | 0.03 | 0.31 | -3.73 | n.a. | |
| Victivallaceae | -1.27 | -1.79 | 0.09 | 0.48 | -4.21 | n.a. |
| [Cerasicoccaceae] | -1.52 | -1.87 | 0.09 | 0.48 | -4.08 | n.a. |
| Family* | logFC | t | P value | FDR | B | sig. Level |
|---|---|---|---|---|---|---|
| Succinivibrionaceae | 2.37 | 2.19 | 0.04 | 0.63 | -4.57 | n.s. |
| Dehalobacteriaceae | 1.80 | 2.50 | 0.02 | 0.58 | -4.56 | n.s. |
| no match | 0.96 | 1.92 | 0.06 | 0.63 | -4.52 | n.s. |
| Christensenellaceae | 0.93 | 1.67 | 0.10 | 0.63 | -4.56 | n.s. |
| Rikenellaceae | 0.85 | 1.34 | 0.19 | 0.63 | -4.57 | n.s. |
| [Barnesiellaceae] | 0.74 | 1.22 | 0.23 | 0.63 | -4.58 | n.s. |
| Erysipelotrichaceae | 0.60 | 1.50 | 0.14 | 0.63 | -4.56 | n.s. |
| Turicibacteraceae | 0.55 | 0.75 | 0.46 | 0.79 | -4.60 | n.s. |
| Ruminococcaceae | 0.43 | 1.22 | 0.23 | 0.63 | -4.58 | n.s. |
| [Odoribacteraceae] | 0.36 | 0.74 | 0.46 | 0.79 | -4.61 | n.s. |
| Lachnospiraceae | 0.36 | 1.14 | 0.26 | 0.63 | -4.59 | n.s. |
| Pseudomonadaceae | 0.30 | 0.62 | 0.54 | 0.82 | -4.61 | n.s. |
| Porphyromonadaceae | 0.30 | 0.66 | 0.51 | 0.81 | -4.61 | n.s. |
| Bacteroidaceae | 0.30 | 0.71 | 0.48 | 0.79 | -4.61 | n.s. |
| Clostridiaceae | 0.29 | 0.70 | 0.49 | 0.79 | -4.61 | n.s. |
| S24-7 | 0.22 | 0.40 | 0.69 | 0.90 | -4.61 | n.s. |
| Leptotrichiaceae | 0.19 | 0.19 | 0.85 | 0.96 | -4.60 | n.s. |
| Aerococcaceae | 0.18 | 0.16 | 0.87 | 0.96 | -4.60 | n.s. |
| Peptococcaceae | 0.17 | 0.26 | 0.80 | 0.93 | -4.60 | n.s. |
| Caulobacteraceae | 0.14 | 0.31 | 0.76 | 0.93 | -4.61 | n.s. |
| Peptostreptococcaceae | 0.13 | 0.18 | 0.85 | 0.96 | -4.61 | n.s. |
| Oxalobacteraceae | 0.10 | 0.28 | 0.78 | 0.93 | -4.62 | n.s. |
| Verrucomicrobiaceae | 0.07 | 0.10 | 0.92 | 0.97 | -4.61 | n.s. |
| Prevotellaceae | 0.06 | 0.08 | 0.94 | 0.97 | -4.62 | n.s. |
| Pasteurellaceae | 0.01 | 0.03 | 0.98 | 0.98 | -4.62 | n.s. |
| Bradyrhizobiaceae | -0.02 | -0.03 | 0.98 | 0.98 | -4.61 | n.s. |
| Bifidobacteriaceae | -0.06 | -0.12 | 0.91 | 0.97 | -4.62 | n.s. |
| [Mogibacteriaceae] | -0.11 | -0.31 | 0.76 | 0.93 | -4.62 | n.s. |
| Coriobacteriaceae | -0.14 | -0.41 | 0.69 | 0.90 | -4.62 | n.s. |
| Comamonadaceae | -0.16 | -0.46 | 0.65 | 0.89 | -4.62 | n.s. |
| Lactobacillaceae | -0.21 | -0.38 | 0.71 | 0.90 | -4.61 | n.s. |
| Alcaligenaceae | -0.21 | -0.58 | 0.57 | 0.84 | -4.61 | n.s. |
| Desulfovibrionaceae | -0.24 | -0.51 | 0.61 | 0.87 | -4.61 | n.s. |
| Actinomycetaceae | -0.34 | -0.85 | 0.40 | 0.79 | -4.60 | n.s. |
| Sphingomonadaceae | -0.35 | -1.16 | 0.25 | 0.63 | -4.59 | n.s. |
| Neisseriaceae | -0.41 | -0.51 | 0.61 | 0.87 | -4.60 | n.s. |
| Moraxellaceae | -0.50 | -0.87 | 0.39 | 0.79 | -4.60 | n.s. |
| Eubacteriaceae | -0.55 | -0.75 | 0.46 | 0.79 | -4.60 | n.s. |
| Victivallaceae | -0.56 | -0.72 | 0.48 | 0.79 | -4.60 | n.s. |
| Streptococcaceae | -0.59 | -1.17 | 0.25 | 0.63 | -4.59 | n.s. |
| Carnobacteriaceae | -0.64 | -1.47 | 0.15 | 0.63 | -4.57 | n.s. |
| [Weeksellaceae] | -0.69 | -0.92 | 0.37 | 0.78 | -4.60 | n.s. |
| Veillonellaceae | -0.71 | -1.78 | 0.08 | 0.63 | -4.54 | n.s. |
| Enterococcaceae | -0.73 | -1.01 | 0.32 | 0.71 | -4.60 | n.s. |
| [Paraprevotellaceae] | -0.77 | -1.24 | 0.22 | 0.63 | -4.58 | n.s. |
| Staphylococcaceae | -0.78 | -1.16 | 0.26 | 0.63 | -4.59 | n.s. |
| Campylobacteraceae | -0.80 | -1.28 | 0.21 | 0.63 | -4.59 | n.s. |
| [Tissierellaceae] | -0.82 | -1.32 | 0.20 | 0.63 | -4.59 | n.s. |
| Micrococcaceae | -0.83 | -1.24 | 0.23 | 0.63 | -4.59 | n.s. |
| Corynebacteriaceae | -0.88 | -1.29 | 0.21 | 0.63 | -4.59 | n.s. |
| Fusobacteriaceae | -0.99 | -1.78 | 0.09 | 0.63 | -4.57 | n.s. |
| Gemellaceae | -1.00 | -1.69 | 0.10 | 0.63 | -4.58 | n.s. |
| Enterobacteriaceae | -1.21 | -2.40 | 0.02 | 0.58 | -4.50 | n.s. |
| Rhodobacteraceae | -1.32 | -1.09 | 0.29 | 0.67 | -4.59 | n.s. |
| Deinococcaceae | -1.64 | -1.26 | 0.23 | 0.63 | -4.59 | n.s. |
statistics on genus level
soource('table_s4.R')
script generates
results/table_s4_genus_aih_vs_control.tsvtable_s3_genus_aih_vs_helathy.tsvtable_s3_genus_healthy_vs_control.tsv
which was modified manually to create ms/version_september_17/Table_S4.xlsx