Table 2 Proteins differentially expressed between critical and non-critical patients at 10% of false discovery rate (FDR).

From: Biomarker candidates for progression and clinical management of COVID-19 associated pneumonia at time of admission

Master protein accession

Protein description

Symbol

Critical vs non-critical

Post-treatment vs pre-treatment

Fold-change

p value

Adjusted p value

Fold-change

p value

Adjusted p value

O00327

Aryl hydrocarbon receptor nuclear translocator-like protein 1 OS = Homo sapiens OX = 9606 GN = ARNTL PE = 1 SV = 2

ARNTL

4.43

 < 2.22e−16

 < 2.22e−16

− 2.29

0.0341

0.0611

P06331

Immunoglobulin heavy variable 4–34 OS = Homo sapiens OX = 9606 GN = IGHV4-34 PE = 1 SV = 2

IGHV4-34

− 3.58

0.0000

0.0003

13.34

0.0000

0.0000

Q86UD1

Out at first protein homolog OS = Homo sapiens OX = 9606 GN = OAF PE = 2 SV = 1

OAF

2.17

0.0000

0.0008

− 1.50

0.0310

0.0571

A0A0B4J1V2

Immunoglobulin heavy variable 2–26 OS = Homo sapiens OX = 9606 GN = IGHV2-26 PE = 3 SV = 1

IGHV2-26

−2.11

0.0042

0.0520

− 1.37

0.1413

0.2117

P61769

Beta-2-microglobulin OS = Homo sapiens OX = 9606 GN = B2M PE = 1 SV = 1

B2M

2.04

0.0001

0.0016

1.73

0.0007

0.0017

P01721

Immunoglobulin lambda variable 6–57 OS = Homo sapiens OX = 9606 GN = IGLV6-57 PE = 1 SV = 2

IGLV6-57

− 2.01

0.0000

0.0000

− 1.19

0.5102

0.6062

P01717

Immunoglobulin lambda variable 3–25 OS = Homo sapiens OX = 9606 GN = IGLV3-25 PE = 1 SV = 2

IGLV3-25

− 1.95

0.0094

0.0847

− 1.13

0.8369

0.8778

P01861

Immunoglobulin heavy constant gamma 4 OS = Homo sapiens OX = 9606 GN = IGHG4 PE = 1 SV = 1

IGHG4

1.85

0.0005

0.0091

− 2.43

0.0000

0.0000

Q9NTG1

Polycystic kidney disease and receptor for egg jelly-related protein OS = Homo sapiens OX = 9606 GN = PKDREJ PE = 2 SV = 2

PKDREJ

1.80

0.0062

0.0667

− 1.59

0.0104

0.0212

Q9UP83

Conserved oligomeric Golgi complex subunit 5 OS = Homo sapiens OX = 9606 GN = COG5 PE = 1 SV = 3

COG5

− 1.74

0.0000

0.0000

1.33

0.0000

0.0001

Q6EMK4

Vasorin OS = Homo sapiens OX = 9606 GN = VASN PE = 1 SV = 1

VASN

1.72

0.0074

0.0704

−

−

–

P01834

Immunoglobulin kappa constant OS = Homo sapiens OX = 9606 GN = IGKC PE = 1 SV = 2

IGKC

1.72

0.0000

0.0000

− 2.17

0.0009

0.0023

P01591

Immunoglobulin J chain OS = Homo sapiens OX = 9606 GN = JCHAIN PE = 1 SV = 4

JCHAIN

− 1.68

0.0024

0.0351

− 1.36

0.0150

0.0292

P0CG40

Transcription factor Sp9 OS = Homo sapiens OX = 9606 GN = SP9 PE = 3 SV = 1

SP9

1.63

0.0003

0.0073

− 4.82

 < 2.22e−16

 < 2.22e−16

P00746

Complement factor D OS = Homo sapiens OX = 9606 GN = CFD PE = 1 SV = 5

CFD

1.61

0.0010

0.0168

− 1.12

0.2556

0.3386

P0DOY2

Immunoglobulin lambda constant 2 OS = Homo sapiens OX = 9606 GN = IGLC2 PE = 1 SV = 1

IGLC2

1.55

0.0011

0.0177

2.42

0.0013

0.0032

P0DP01

Immunoglobulin heavy variable 1–8 OS = Homo sapiens OX = 9606 GN = IGHV1-8 PE = 3 SV = 1

IGHV1-8

− 1.52

0.0037

0.0495

1.07

0.8190

0.8703

Q9Y6K5

2′-5′-oligoadenylate synthase 3 OS = Homo sapiens OX = 9606 GN = OAS3 PE = 1 SV = 3

OAS3

− 1.48

0.0000

0.0000

1.45

0.0002

0.0006

P02655

Apolipoprotein C-II OS = Homo sapiens OX = 9606 GN = APOC2 PE = 1 SV = 1

APOC2

1.47

0.0055

0.0644

1.34

0.1703

0.2438

A0A075B6R9

Probable non-functional immunoglobulin kappa variable 2D-24 OS = Homo sapiens OX = 9606 GN = IGKV2D-24 PE = 5 SV = 1

IGKV2D-24

− 1.42

0.0011

0.0179

− 1.50

0.0518

0.0878

P08571

Monocyte differentiation antigen CD14 OS = Homo sapiens OX = 9606 GN = CD14 PE = 1 SV = 2

CD14

1.42

0.0023

0.0350

1.89

0.0000

0.0000

P01701

Immunoglobulin lambda variable 1–51 OS = Homo sapiens OX = 9606 GN = IGLV1-51 PE = 1 SV = 2

IGLV1-51

− 1.40

0.0074

0.0704

− 1.01

0.9625

0.9685

P01859

Immunoglobulin heavy constant gamma 2 OS = Homo sapiens OX = 9606 GN = IGHG2 PE = 1 SV = 2

IGHG2

1.40

0.0000

0.0001

− 1.59

0.0022

0.0051

P02538

Keratin, type II cytoskeletal 6A OS = Homo sapiens OX = 9606 GN = KRT6A PE = 1 SV = 3

KRT6A

− 1.39

0.0107

0.0937

− 1.38

0.5156

0.6104

A0A075B6I9

Immunoglobulin lambda variable 7–46 OS = Homo sapiens OX = 9606 GN = IGLV7-46 PE = 3 SV = 4

IGLV7-46

1.38

0.0004

0.0087

− 2.25

0.0000

0.0000

Q9UGM5

Fetuin-B OS = Homo sapiens OX = 9606 GN = FETUB PE = 1 SV = 2

FETUB

1.38

0.0000

0.0000

1.11

0.2627

0.3453

P02787

Serotransferrin OS = Homo sapiens OX = 9606 GN = TF PE = 1 SV = 3

TF

1.37

0.0000

0.0000

− 1.14

0.0192

0.0371

P02768

Serum albumin OS = Homo sapiens OX = 9606 GN = ALB PE = 1 SV = 2

ALB

1.37

0.0000

0.0001

− 1.07

0.1371

0.2073

P35858

Insulin-like growth factor-binding protein complex acid labile subunit OS = Homo sapiens OX = 9606 GN = IGFALS PE = 1 SV = 1

IGFALS

1.35

0.0067

0.0687

1.07

0.2830

0.3674

P00738

Haptoglobin OS = Homo sapiens OX = 9606 GN = HP PE = 1 SV = 1

HP

1.35

0.0000

0.0000

− 1.24

0.0420

0.0735

P06396

Gelsolin OS = Homo sapiens OX = 9606 GN = GSN PE = 1 SV = 1

GSN

1.33

0.0006

0.0112

− 1.03

0.5348

0.6308

P02647

Apolipoprotein A-I OS = Homo sapiens OX = 9606 GN = APOA1 PE = 1 SV = 1

APOA1

1.30

0.0047

0.0563

1.07

0.2197

0.2972

P02656

Apolipoprotein C-III OS = Homo sapiens OX = 9606 GN = APOC3 PE = 1 SV = 1

APOC3

1.29

0.0059

0.0667

− 1.10

0.5091

0.6062

P02671

Fibrinogen alpha chain OS = Homo sapiens OX = 9606 GN = FGA PE = 1 SV = 2

FGA

1.24

0.0115

0.0961

1.39

0.0000

0.0000

Q04756

Hepatocyte growth factor activator OS = Homo sapiens OX = 9606 GN = HGFAC PE = 1 SV = 1

HGFAC

1.23

0.0081

0.0749

− 1.47

0.0045

0.0101

A0A0C4DH35

Probable non-functional immunoglobulin heavy variable 3–35 OS = Homo sapiens OX = 9606 GN = IGHV3-35 PE = 5 SV = 1

IGHV3-35

− 1.21

0.0111

0.0943

− 1.11

0.2434

0.3280

Q9NZP8

Complement C1r subcomponent-like protein OS = Homo sapiens OX = 9606 GN = C1RL PE = 1 SV = 2

C1RL

1.20

0.0063

0.0667

1.12

0.1735

0.2462

P02774

Vitamin D-binding protein OS = Homo sapiens OX = 9606 GN = GC PE = 1 SV = 2

GC

1.19

0.0003

0.0074

1.19

0.0006

0.0015

P00751

Complement factor B OS = Homo sapiens OX = 9606 GN = CFB PE = 1 SV = 2

CFB

1.19

0.0000

0.0000

1.89

0.0000

0.0000

P04217

Alpha-1B-glycoprotein OS = Homo sapiens OX = 9606 GN = A1BG PE = 1 SV = 4

A1BG

1.17

0.0041

0.0520

1.27

0.0000

0.0000

P01042

Kininogen-1 OS = Homo sapiens OX = 9606 GN = KNG1 PE = 1 SV = 2

KNG1

1.17

0.0069

0.0693

1.09

0.2509

0.3367

P04180

Phosphatidylcholine-sterol acyltransferase OS = Homo sapiens OX = 9606 GN = LCAT PE = 1 SV = 1

LCAT

1.17

0.0033

0.0455

1.23

0.0263

0.0489

  1. The table also shows the results from the analysis comparing Treated and Not-treated samples for the same proteins. Results are derived from a linear mixed-effects model fitted to each protein independently that included peptide and patient as random effects. Digestion batch, evolution group (critical/non-critical), blood extraction day and the interaction of the two latter were modelled as fixed effects. Comparisons were performed by averaging time point estimations within each evolution group. Differences between treatment status were assessed in an analogous way, using a model that included treatment and batch of samples' digestion as fixed effects. Positive fold-changes indicate over-expression in critical patients or in Treated samples while negative fold-changes represent over-expression in non-critical patients or in Not-treated samples, respectively. Statistical significance was assessed using a Wald test derived from the models. The Benjamini–Hochberg method was used for control of the FDR (Adjusted p value).
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