Table 6 List of differentially expressed genes with at least twofold change obtained from comparisons of no recurrence vs recurrence in the TNT group

From: Breast carcinoma with amplified HER2: a gene expression signature specific for trastuzumab resistance and poor prognosis

Illumina ID

Log2 FC

P-value

ENTREZ

Symbol

Description

Upregulated genes in no recurrence vs recurrence comparisons

ALB

3.40

0.022763

213

ALB

Homo sapiens albumin (ALB), mRNA

LOC647450

2.71

0.014532

647450

LOC647450

Predicted: homo sapiens similar to Ig κ chain V-I region HK101 precursor (LOC647450), mRNA

LOC652493

2.68

0.012371

652493

LOC652493

Predicted: homo sapiens similar to Ig κ chain V-I region HK102 precursor (LOC652493), mRNA

LOC651751

2.57

0.000492

651751

LOC651751

Predicted: homo sapiens similar to Ig κ chain V-II region RPMI 6410 precursor (LOC651751), mRNA

CEACAM6

2.57

0.031912

4680

CEACAM6

Homo sapiens carcinoembryonic antigen-related cell adhesion molecule 6 (nonspecific cross-reacting antigen) (CEACAM6), mRNA

LOC642113

2.41

0.01145

642113

LOC642113

Predicted: homo sapiens similar to Ig κ chain V–III region HAH precursor (LOC642113), mRNA

LOC652694

2.39

0.002864

652694

LOC652694

Predicted: homo sapiens similar to Ig κ chain V–I region HK102 precursor (LOC652694), mRNA

HLA-DRB5

2.38

0.029661

3127

HLA-DRB5

Homo sapiens major histocompatibility complex, class II, DR β 5 (HLA-DRB5), mRNA

LOC649923

2.16

0.006045

649923

LOC649923

Predicted: homo sapiens similar to Ig gamma-2 chain C region (LOC649923), mRNA

LOC652775

2.01

0.002943

652775

LOC652775

Predicted: homo sapiens similar to Ig κ chain V–V region L7 precursor (LOC652775), mRNA

LOC652102

1.74

0.000466

652102

LOC652102

Predicted: homo sapiens similar to Ig heavy chain V–I region HG3 precursor (LOC652102), mRNA

IGLL1

1.62

0.014304

3543

IGLL1

Homo sapiens immunoglobulin λ-like polypeptide 1 (IGLL1), transcript variant 2, mRNA

ACOX2

1.60

0.000967

8309

ACOX2

Homo sapiens acyl-coenzyme A oxidase 2, branched chain (ACOX2), mRNA

MGC29506

1.59

0.014185

51237

MGC29506

Homo sapiens hypothetical protein MGC29506 (MGC29506), mRNA

HLA-DQA1

1.51

0.015729

3117

HLA-DQA1

Predicted: homo sapiens major histocompatibility complex, class II, DQ α 1, transcript variant 10 (HLA-DQA1), mRNA

LYZ

1.47

0.042465

4069

LYZ

Homo sapiens lysozyme (renal amyloidosis) (LYZ), mRNA

HLA-DRB4

1.46

0.013791

3126

HLA-DRB4

Homo sapiens major histocompatibility complex, class II, DR β 4 (HLA-DRB4), mRNA

HLA-DRA

1.44

0.023102

3122

HLA-DRA

Homo sapiens major histocompatibility complex, class II, DR α (HLA-DRA), mRNA

SLC5A1

1.39

0.021721

6523

SLC5A1

Homo sapiens solute carrier family 5 (sodium/glucose cotransporter), member 1 (SLC5A1), mRNA

HLA-DMA

1.39

0.009901

3108

HLA-DMA

Homo sapiens major histocompatibility complex, class II, DM α (HLA-DMA), mRNA

GZMK

1.36

0.014311

3003

GZMK

Homo sapiens granzyme K (granzyme 3; tryptase II) (GZMK), mRNA

C6ORF192

1.34

0.027143

116843

C6ORF192

Homo sapiens chromosome 6 open reading frame 192 (C6orf192), mRNA

SOSTDC1

1.30

0.007454

25928

SOSTDC1

Homo sapiens sclerostin domain containing 1 (SOSTDC1), mRNA

MGP

1.24

0.047067

4256

MGP

Homo sapiens matrix Gla protein (MGP), mRNA

LOC644151

1.24

0.013498

644151

LOC644151

Predicted: homo sapiens similar to calpain 8 (LOC644151), mRNA

CAMK1G

1.21

0.00353

57172

CAMK1G

Homo sapiens calcium/calmodulin-dependent protein kinase IG (CAMK1G), mRNA

HLA-DRB3

1.21

0.016937

3125

HLA-DRB3

Homo sapiens major histocompatibility complex, class II, DR β 3 (HLA-DRB3), mRNA

FAM46C

1.20

0.020803

54855

FAM46C

Homo sapiens family with sequence similarity 46, member C (FAM46C), mRNA

HLA-DMB

1.18

0.009027

3109

HLA-DMB

Homo sapiens major histocompatibility complex, class II, DM β (HLA-DMB), mRNA

CFD

1.17

0.043992

1675

CFD

Homo sapiens complement factor D (adipsin) (CFD), mRNA

VIPR1

1.17

0.007108

7433

VIPR1

Homo sapiens vasoactive intestinal peptide receptor 1 (VIPR1), mRNA

JSRP1

1.16

0.000782

126306

JSRP1

Homo sapiens junctional sarcoplasmic reticulum protein 1 (JSRP1), mRNA

HLA-DRB6

1.14

0.037486

3128

HLA-DRB6

Homo sapiens major histocompatibility complex, class II, DR β 6 (pseudogene) (HLA-DRB6), non-coding RNA

CPVL

1.09

0.022705

54504

CPVL

Homo sapiens carboxypeptidase, vitellogenic-like (CPVL), transcript variant 1, mRNA

MYB

1.08

0.026033

4602

MYB

Homo sapiens v-myb myeloblastosis viral oncogene homolog (avian) (MYB), transcript variant 2, mRNA

PIM2

1.05

0.002093

11040

PIM2

Homo sapiens pim-2 oncogene (PIM2), mRNA

CD79A

1.01

0.005757

973

CD79A

Homo sapiens CD79a molecule, immunoglobulin-associated α (CD79A), transcript variant 1, mRNA

LPXN

1.01

0.015139

9404

LPXN

Homo sapiens leupaxin (LPXN), mRNA

Downregulated genes no recurrence vs recurrence comparisons

CASC3

−1.10

0.04282

22794

CASC3

Homo sapiens cancer susceptibility candidate 3 (CASC3), mRNA

SNCG

−1.26

0.00869

6623

SNCG

Homo sapiens synuclein, gamma (breast cancer-specific protein 1) (SNCG), mRNA

HIST1H2BD

−1.35

0.008322

3017

HIST1H2BD

Homo sapiens histone cluster 1, H2bd (HIST1H2BD), transcript variant 2, mRNA

HIST1H4H

−1.52

0.005711

8365

HIST1H4H

Homo sapiens histone cluster 1, H4 h (HIST1H4H), mRNA

ERBB2

−1.66

0.037147

2064

ERBB2

Homo sapiens v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) (ERBB2), transcript variant 2, mRNA

PNMT

−1.87

0.028033

5409

PNMT

Homo sapiens phenylethanolamine N-methyltransferase (PNMT), mRNA

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