Table 2 List of 58 proteins differentially expressed in LN positive GBC. This includes 53 proteins specific to LN positive GBC (A) and 5 proteins showed opposite correlation in expression among the proteins common to both the stages (B). The detailed protein and peptide list is provided in Supplementary Table S1

(A)

 A1BG

Alpha-1B-glycoprotein precursor

1.296

0.538

0.51

0.447

0.581

0.883

0.734

 ADH1C

Alcohol dehydrogenase 1C

0.809

4.096

1.362

0.486

0.656

0.627

0.448

 AGR2

Anterior gradient protein 2

0.99

0.53

1.998

1.582

4.208

1.685

0.712

 ALDH18A1

Delta-1-pyrroline-5-carboxylate synthase isoform X1

1.126

0.867

1.471

3.227

1.416

0.927

1.246

 ANP32A

Acidic leucine-rich nuclear phosphoprotein 32 family member A

0.845

0.808

1.534

2.300

1.439

1.214

1.219

 ANXA10

Annexin A10 isoform X1

0.886

1.017

1.623

4.130

1.087

1.283

0.889

 AOC3

Membrane primary amine oxidase isoform X1

0.559

0.749

0.856

0.50

0.733

0.703

0.485

 APEX1

DNA-(apurinic or apyrimidinic site) lyase

1.372

0.688

1.223

2.057

1.462

1.311

1.311

 APOC3

Apolipoprotein C-III precursor

0.68

1.408

0.466

0.165

0.158

0.109

0.245

 CAPG

Macrophage-capping protein isoform X1

1.274

0.606

0.877

1.363

1.103

1.402

2.061

 CKMT1A

Creatine kinase U-type, mitochondrial isoform 1 precursor

1.163

0.786

1.367

3.211

1.695

1.445

1.014

 COL1A2

Collagen alpha-2(I) chain precurso

0.677

0.654

0.623

0.520

0.486

0.563

0.621

 COX4I1

Cytochrome c oxidase subunit 4 isoform 1, mitochondrial isoform X1

0.712

1.593

1.013

2.687

1.265

0.843

1.012

 COX5A

Cytochrome c oxidase subunit 5A, mitochondrial precursor

0.652

1.782

1.321

2.817

1.397

0.894

1.006

 COX6B1

Cytochrome c oxidase subunit 6B1

0.891

1.431

1.406

2.289

1.047

1.140

0.977

 DLST

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial isoform 1 precursor

0.756

1.553

1.66

3.701

2.754

0.988

1.215

 ECH1

Delta(3,5)-Delta(2,4)-dienoyl-coa isomerase, mitochondrial isoform X1

0.934

1.796

1.434

1.135

2.459

0.993

0.957

 EEF1A1

Elongation factor 1-alpha 1

0.665

1.741

1.307

2.511

1.817

0.666

3.143

 FABP5

Fatty acid-binding protein 5

0.895

0.545

1.464

0.827

1.438

1.035

8.795

 GMDS

GDP-mannose 4,6 dehydratase isoform 1

1.033

0.937

1.398

3.061

0.816

0.937

0.853

 HADHB

Trifunctional enzyme subunit beta, mitochondrial isoform X1

0.988

1.565

1.457

2.118

1.514

0.995

1.093

 HNRNPA1

Heterogeneous nuclear ribonucleoprotein A1 isoform X1

0.618

0.813

1.613

3.609

3.282

1.135

2.160

 HNRNPA2B1

Heterogeneous nuclear ribonucleoproteins A2/B1 isoform X1

0.523

0.831

1.256

2.594

2.939

0.807

2.714

 HNRNPA3

Heterogeneous nuclear ribonucleoprotein A3 isoform a

0.699

0.659

1.356

1.376

3.393

0.672

2.360

 HNRNPK

Heterogeneous nuclear ribonucleoprotein K isoform X1

0.91

0.816

1.922

2.541

2.434

1.183

2.334

 HSP90AA1

Heat shock protein HSP 90-alpha isoform 1

0.743

0.976

1.611

1.744

2.088

1.139

1.574

 HSP90AB1

Heat shock protein HSP 90-beta isoform X1

0.802

0.858

1.903

2.421

1.800

1.345

2.728

 HSPA8

Heat shock cognate 71 kda protein isoform X1

0.712

1.162

1.067

1.588

1.588

1.726

2.270

 HSPA9

Stress-70 protein, mitochondrial precursor

0.796

1.664

1.656

3.183

2.044

1.037

2.357

 IDH2

Isocitrate dehydrogenase [NADP], mitochondrial isoform 1 precursor

1.011

1.722

1.231

2.148

1.310

0.744

1.181

 KRT1

Keratin, type II cytoskeletal 1

1.418

0.585

0.606

0.473

0.768

0.611

0.897

 KRT17

Keratin, type I cytoskeletal 17

1.088

0.765

1.091

0.827

1.556

4.911

7.180

 KRT19

Keratin, type I cytoskeletal 19

1.002

0.749

1.788

7.241

3.853

2.390

0.930

 KRT6A

Keratin, type II cytoskeletal 6A

1.252

0.732

1.397

1.202

0.888

1.352

2.212

 KRT7

Keratin, type II cytoskeletal 7

0.878

0.72

0.963

2.651

1.944

2.497

0.820

 LASP1

LIM and SH3 domain protein 1 isoform a

1.531

1.045

1.107

2.971

1.467

0.881

1.703

 LRPPRC

Leucine-rich PPR motif-containing protein, mitochondrial precursor

1.312

0.659

1.544

3.315

2.019

0.905

1.217

 MDH2

Malate dehydrogenase, mitochondrial isoform 1 precursor

0.797

1.519

1.651

3.556

2.404

1.465

1.694

 NPM1

Nucleophosmin isoform 1

0.72

1.224

1.131

3.362

0.835

1.725

2.930

 PGD

6-phosphogluconate dehydrogenase, decarboxylating isoform 1

1.811

0.967

1.04

1.270

1.084

1.132

2.052

 PKM

Pyruvate kinase PKM isoform c

0.9

0.599

1.345

2.065

1.333

1.416

1.940

 PPIA

Peptidyl-prolyl cis–trans isomerase A isoform 1

0.733

0.908

1.3

1.778

1.747

1.446

2.435

 PPIB

Peptidyl-prolyl cis–trans isomerase B precursor

0.746

1.261

1.31

1.577

1.066

1.279

2.299

 RPS28

40S ribosomal protein S28

0.82

1.712

1.642

2.046

1.871

0.681

2.114

 SERPINH1

Serpin H1 isoform X1

0.988

0.881

1.269

1.046

1.450

1.061

2.587

 SLC25A3

Phosphate carrier protein, mitochondrial isoform a precursor

0.975

1.608

2.098

2.371

1.585

0.895

1.314

 SLC25A6

ADP/ATP translocase 3

1.247

1.422

1.776

2.021

1.701

0.950

1.430

 SRI

Sorcin isoform A

0.868

0.753

1.011

0.828

2.380

2.394

0.941

 TAGLN2

Transgelin-2 isoform

0.566

0.535

0.634

0.965

1.624

1.629

2.082

 TUFM

Elongation factor Tu, mitochondrial isoform 1 precursor

0.975

0.828

1.582

3.457

1.009

0.803

1.609

 TYMP

Thymidine phosphorylase isoform 1 precursor

1.97

1.138

1.024

0.905

1.045

1.252

2.441

 VCAN

Versican core protein isoform 1 precursor

0.626

0.725

0.895

0.690

1.059

3.567

0.807

 VIM

Vimentin

0.686

0.522

0.685

0.387

0.863

1.376

1.479

(B)

 ADH4

Alcohol dehydrogenase 4 isoform 1

0.50

9.87

2.15

0.49

0.50

0.47

0.43

 ANXA2

Annexin A2 isoform 1

0.54

0.47

0.58

1.51

1.29

2.94

2.09

 ANXA5

Annexin A5

0.76

0.40

0.52

1.60

1.17

2.75

1.15

 RDH16

Retinol dehydrogenase 16 isoform 1

0.53

3.57

3.54

0.68

0.49

0.39

0.50

 UGT2B7

UDP-glucuronosyltransferase 2B7 isoform 1 precursor

0.49

3.62

1.34

0.68

0.49

0.38

0.37