Table 5 MaAsLin2-derived significant gene ontologies associated with COVID-19 disease outcome (deceased vs. survived).

From: Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease

Name

Ontology

Namespace

Depth

Coef

Stderr

pval

qval

N

Samples w/ > 0 counts

Pyrimidine-containing compound metabolic process

Biological_process

GO:0072527

4

−4.815

0.867

 < 0.001

 < 0.001

25

12

Nucleobase-containing compound biosynthetic process

Biological_process

GO:0034654

5

−0.630

0.117

 < 0.001

 < 0.001

25

25

Transition metal ion binding

Molecular_function

GO:0046914

5

−0.545

0.106

 < 0.001

 < 0.001

25

25

Aromatic compound biosynthetic process

Biological_process

GO:0019438

4

−0.478

0.116

 < 0.001

0.004

25

25

Heterocycle biosynthetic process

Biological_process

GO:0018130

4

−0.393

0.100

 < 0.001

0.007

25

25

Macromolecule biosynthetic process

Biological_process

GO:0009059

4

0.382

0.103

 < 0.001

0.015

25

25

RNA metabolic process

Biological_process

GO:0016070

6

−0.310

0.086

 < 0.001

0.018

25

25

RNA phosphodiester bond hydrolysis

Biological_process

GO:0090501

7

−1.412

0.402

 < 0.001

0.024

25

17

Magnesium ion binding

Molecular_function

GO:0000287

5

−2.336

0.709

0.001

0.036

25

11

RNA binding

Molecular_function

GO:0003723

4

0.989

0.303

0.001

0.036

25

23

Zinc ion binding

Molecular_function

GO:0008270

6

−0.880

0.266

0.001

0.036

25

24

Phosphorylation

Biological_process

GO:0016310

5

2.897

0.888

0.001

0.036

25

13

Organonitrogen compound catabolic process

Biological_process

GO:1901565

4

−2.388

0.721

0.001

0.036

25

12

Endopeptidase activity

Molecular_function

GO:0004175

4

−0.995

0.309

0.001

0.037

25

21

Pyrimidine-containing compound biosynthetic process

Biological_process

GO:0072528

5

−5.505

1.711

0.001

0.037

25

7

DNA recombination

Biological_process

GO:0006310

7

−2.130

0.667

0.001

0.037

25

12

oxidoreductase activity

Molecular_function

GO:0016491

2

2.541

0.801

0.002

0.037

25

13

Carbohydrate metabolic process

Biological_process

GO:0005975

3

2.245

0.717

0.002

0.039

25

15

Catalytic activity, acting on RNA

Molecular_function

GO:0140098

2

−0.546

0.174

0.002

0.039

25

25

Pyrophosphatase activity

Molecular_function

GO:0016462

5

−0.326

0.107

0.002

0.048

25

25

Organic cyclic compound binding

Molecular_function

GO:0097159

2

0.443

0.145

0.002

0.048

25

25

Hydrolase activity, acting on acid anhydrides

Molecular_function

GO:0016817

3

−0.323

0.107

0.003

0.052

25

25

  1. Comparisons were conducted using compositional transformed and CLR normalized count matrices, controlled for the random effect of patient ID, and adjusted for multiple test comparisons using the Benajmini Hochberg correction method. A full list of statistically significant GO terms in COVID-19 Deceased vs. Survived can be found in Suppl. Table 4.
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