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Table 1 Gene set enrichment analysis for genes ranked according to odds of infection recurrence. Size – total size of pathway in tested dataset, ES – enrichment score, NES – normalized enrichment score, pvalue – p-value in GSEA analysis (permutation test), padjust – pvalue after adjustment for multiple testing, rank – rank with peak enrichment score, core enrichment – gene names (if available) present in core enrichment. Adjusted p-values < 0.05 were considered significant

From: Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection

ID

Description

setSize

ES

NES

pvalue

padjust

rank

core enrichment

ko00190

Oxidative phosphorylation

15

0.87

2.12

2.19E-04

1.22E-02

160

ntpG/ntpI/atpD/ntpB/ppaC/hydA

ko01200

Carbon metabolism

67

0.50

1.71

9.59E-04

2.07E-02

899

ato1/acoB/cooS1/rpiB/fdhF/serA/ppaC/acoC/fwdE/pgk/glcK/fba2/pyc/bcd_1/tal/tklB/pfkB/pgi/dpaL/fbp/nadB/rpe/dpaL/nifJ/gap

ko01120

Microbial metabolism in diverse environments

199

0.37

1.47

1.11E-03

2.07E-02

1245

group_10292/ato1/mngA/acoB/licR/cooS1/rpiB/fdhF/serA/group_3100/group_15830/ppaC/argD/group_10260/acoC/fwdE/group_18370/group_14018/mtlA/pyrK/group_14004/group_20309/pgk/hemB/glcK/fba2/pyc/cobA/leuC/group_7776/bcd_1/group_1934/dfa1/group_12907/group_4079/tal/group_11132/tklB/lysC/rnhA/pfkB/group_11374/pgi/group_7372/group_11044/fbp/nadB/group_607/asrA/asrB/MA20_09190/rpe/group_12912/thrC/group_1435/group_1680/nifJ/gap/hom/rnhA/adhE/xdhA1/fucA/acsD/group_16780/group_14000/asrC/group_7768/icd/ytjP/sucD/group_16251/group_8676/rpiB/gutB/algC/gatB/hom/rpe/cooS1/group_18922/pmmB/group_18142

ko03010

Ribosome

25

0.66

1.82

1.58E-03

2.20E-02

636

rpsK/rpsS/rpsE/rpsL/rplO/rplB/rplA/rpmH/rpmD

ko01130

Biosynthesis of antibiotics

118

0.41

1.53

3.07E-03

3.10E-02

922

dxs/ato-1/acoB/ispD/rpiB/serA/argD/group_10260/lysN/acoC/purH/aspC/pgk/ilvC/glcK/fba2/argJ/group_7776/galU/tal/tklB/lysC/pabC/pfkB/group_11374/ilvB/pgi/group_7372/dpaL/glmS/argB/fbp/nadB/argC/rpe/dpaL/nifJ/gap/hom/group_15453

ko01210

2-Oxocarboxylic acid metabolism

19

0.68

1.77

3.33E-03

3.10E-02

799

argD/lysN/aspC/ilvC/argJ/leuC/lysC/pabC/ilvB/argB/argC

ko00710

Carbon fixation in photosynthetic organisms

11

0.78

1.75

4.75E-03

3.79E-02

1223

rpiB/pgk/fba2/tklB/fbp/rpe/gap/rpiB/rpe