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Molecular Medicine

, Volume 13, Issue 1–2, pp 40–58 | Cite as

Molecular Profile of Peripheral Blood Mononuclear Cells from Patients with Rheumatoid Arthritis

  • Christopher J. Edwards
  • Jeffrey L. Feldman
  • Jonathan Beech
  • Kathleen M. Shields
  • Jennifer A. Stover
  • William L. Trepicchio
  • Glenn Larsen
  • Brian M. J. Foxwell
  • Fionula M. Brennan
  • Marc Feldmann
  • Debra D. Pittman
Open Access
Research Article

Abstract

Rheumatoid arthritis (RA) is a chronic inflammatory arthritis. Currently, diagnosis of RA may take several weeks, and factors used to predict a poor prognosis are not always reliable. Gene expression in RA may consist of a unique signature. Gene expression analysis has been applied to synovial tissue to define molecularly distinct forms of RA; however, expression analysis of tissue taken from a synovial joint is invasive and clinically impractical. Recent studies have demonstrated that unique gene expression changes can be identified in peripheral blood mononuclear cells (PBMCs) from patients with cancer, multiple sclerosis, and lupus. To identify RA disease-related genes, we performed a global gene expression analysis. RNA from PBMCs of 9 RA patients and 13 normal volunteers was analyzed on an oligonucleotide array. Compared with normal PBMCs, 330 transcripts were differentially expressed in RA. The differentially regulated genes belong to diverse functional classes and include genes involved in calcium binding, chaperones, cytokines, transcription, translation, signal transduction, extracellular matrix, integral to plasma membrane, integral to intracellular membrane, mitochondrial, ribosomal, structural, enzymes, and proteases. A k-nearest neighbor analysis identified 29 transcripts that were preferentially expressed in RA. Ten genes with increased expression in RA PBMCs compared with controls mapped to a RA susceptibility locus, 6p21.3. These results suggest that analysis of RA PBMCs at the molecular level may provide a set of candidate genes that could yield an easily accessible gene signature to aid in early diagnosis and treatment.

Introduction

Rheumatoid arthritis (RA) is a chronic inflammatory disease causing synovial joint damage, disability, and a shortened life expectancy (1,2). An awareness of the destructive potential of RA has led to more aggressive use of disease-modifying anti-rheumatic drugs (DMARDs) (3) and the development of immune therapies targeted to molecules and cells important in the pathogenesis of RA. These include the TNF inhibitors infliximab, etanercept, and adalimumab (4). Synovial joint damage occurs early in the disease course, and many patients demonstrate erosions within a few months after becoming symptomatic (5). Recent evidence suggests that early aggressive therapy (infliximab and methotrexate) yields greater benefit than similar therapy after failure of other drugs (6, 7, 8). To initiate early aggressive therapy requires reliable and rapid determination of diagnosis and prognosis. In addition, factors used to predict a poor prognosis, including sex, age of onset, multiple joint involvement, rheumatoid factor, and the presence of the shared epitope of HLA-DR4, are not always reliable (9, 10, 11, 12).

Gene expression profiling may allow early diagnosis, aid in identifying factors that predict poor prognosis, and help focus early, aggressive, and expensive therapy to those that would benefit the most. Expression analysis of tissues taken at the site of disease within a synovial joint is invasive and impractical on a routine basis. However, recent studies have demonstrated unique gene expression changes in peripheral blood mononuclear cells (PBMCs) from patients with cancer, multiple sclerosis, and lupus (13, 14, 15, 16, 17). In this study, a genomewide scan of PBMCs from normal volunteers and RA PBMCs was performed using oligonucleotide arrays representing 6800 human genes to explore gene expression in the PBMCs of individuals with RA.

Materials and Methods

Patient Selection

Patients with RA, defined by American College of Rheumatology (ACR) criteria (18), were identified in a rheumatology clinic with approval from the local research ethics committee. Demographic data including age, sex, and time since diagnosis were collected. A tender joint count (TJC 0–28), swollen joint count (JC 0–28), patient’s best global assessment (visual analog scale), and erythrocyte sedimentation rate (ESR) were performed to calculate a 28-joint disease activity score (DAS28). The presence of rheumatoid factor (RF) and the use of DMARDs were recorded. Blood was also collected from healthy volunteers with no previous diagnosis of RA or other chronic inflammatory diseases.

Isolation of RNA and Preparation of Labeled Hybridization Solutions

An 8-mL sample of venous blood was collected into CPT Vacutainer cell purification tubes (Becton Dickinson, Franklin Lakes, NJ, USA) and refrigerated immediately. Samples were immediately transferred to the laboratory, and PBMCs from the 9 RA and 13 normal volunteers were separated according to the manufacturer’s recommendations. Briefly, the tube was centrifuged at 1500g (2700 rpm) at room temperature, and PBMCs were isolated before being washed twice in PBS. Total RNA was extracted using the RNeasy minikit (Qiagen, Valencia, CA, USA). For each sample, 2 µg total RNA was used to generate cDNA as described (19). RNA quality was determined by observing distinct 28S and 18S ribosomal bands on an agarose gel. First-strand cDNA synthesis was performed under the following buffer conditions: 1× 1st-strand buffer (Invitrogen Life Technologies, Carlsbad, CA, USA), 10 mM DTT (Gibco/Invitrogen), 500 µM of each dNTP (Invitrogen Life Technologies), 400 units Superscript RT II (Invitrogen Life Technologies), and 40 units RNase inhibitor (Ambion, Austin, TX, USA). The reaction proceeded at 47°C for 1 h. Second-strand cDNA was synthesized with the addition of the following reagents at the final concentrations listed: 1× 2nd-strand buffer (Invitrogen Life Technologies), an additional 200 µM of each dNTP (Invitrogen Life Technologies), 40 units E. coli DNA polymerase I (Invitrogen Life Technologies), 2 units E. coli RNaseH (Invitrogen Life Technologies), and 10 units E. coli DNA ligase. The reaction proceeded at 15°C for 2 h; during the last 5 min of this reaction, 6 units T4 DNA polymerase (New England Biolabs, Beverly, MA, USA) was added. The resulting double-stranded cDNA was purified with the use of BioMag carboxyl-terminated particles as follows: 0.2 mg BioMag particles (Polysciences, Warrington, PA, USA) were equilibrated by washing three times with 0.5 M EDTA and resuspended at a concentration of 22.2 mg/mL in 0.5 M EDTA. The double-stranded cDNA reaction was diluted to a final concentration of 10% PEG/1.25 M NaCl, and the bead suspension was added to a final bead concentration of 0.614 mg/mL. The reaction was incubated at room temperature for 10 min. The cDNA/bead complexes were washed with 300 µL of 70% ethanol, the ethanol was removed, and the tubes were allowed to air dry. The cDNA was eluted with the addition of 20 µL of 10 mM Tris-acetate, pH 7.8, and incubated for 2 to 5 min, and the cDNA-containing supernatant was removed.

Purified double stranded cDNA (10 µL) was added to an in vitro transcription (IVT) solution which contained 1× IVT buffer (Ambion), 5000 units T7 RNA polymerase (Epicentre Technologies, Madison, WI, USA), 3mM GTP, 1.5 mM ATP, 1.2 mM CTP, and 1.2 mM UTP (Amersham/Pharmacia), 0.4 mM each bio-16 UTP and bio-11 CTP (Enzo Diagnostics, Farmingdale, NY, USA), and 80 units RNase inhibitor (Ambion). The reaction proceeded at 37°C for 16 h. Labeled RNA was purified with the use of an RNeasy kit (Qiagen). The RNA yield was quantified by measuring absorbance at 260 nm.

Hybridization to Affymetrix Microarrays and Detection of Fluorescence

Eleven in vitro synthesized transcripts from segments of bacterial genes were included in each hybridization reaction to generate a global standard curve to normalize the oligonucleotide microarrays to each other and estimate the sensitivity of the arrays (20). Purified biotinylated cRNA (10 µg) was hybridized to oligonucleotide arrays comprised of 6937 human gene qualifiers (human FL6800 array P/N900183, Affymetrix, Santa Clara, CA).

Raw fluorescent intensity values were collected and reduced with GeneChip v3.2 software (Affymetrix) as described (Affymetrix GeneChip Analysis Suite User Guide). This determined the probability of each gene qualifier represented on the array being absent, present, or marginal, as well as calculating a specific hybridization intensity value, or average difference, for each transcript. The relative abundances of the 11 bacterial control cRNA transcripts ranged from 1:300,000 (3 ppm) to 1:1000 (1000 ppm) stated in terms of the number of control transcripts per total transcripts. As determined by the signal response from these control transcripts, the sensitivity of detection of the arrays ranged between ∼1:300,000 and 1:100,000 copies/million. The average difference for each transcript was normalized to frequency values as described (20).

Transcripts designated absent in all samples were excluded from the analysis; 3295 (49%) of the transcripts remained. Further analysis of the processed data was performed with GeneSpring version 7.1 (Agilent Technologies, Redwood City, CA, USA). To identify transcripts that were increased in the RA samples compared with controls, >50% (at least 5 of 9) of the samples had to be called present, with a frequency of 10 ppm or greater, and have a change in expression, relative to the average expression of the controls, of at least 2-fold. The resulting data set had 324 gene qualifiers. To find gene qualifiers whose expression was decreased, a list was generated of gene qualifiers from normal samples that were called present with a frequency of ≥10 ppm. The resulting list was filtered for an average decrease in expression, relative to the controls, of at least 2-fold in the disease samples. Six gene qualifiers met these criteria; 330 transcripts were used for the analyses. Annotation for each gene was determined based on GO, Entrez Gene, PubMed, and literature searches.

Statistical and Clustering Analyses

An unsupervised hierarchical clustering was performed on the 330 genes to group the samples on the basis of similarity of their expression profiles (21). Statistically significant differences in expression were determined using Welch ANOVA (22) coupled with two different multiple testing corrections. The Benjamini and Hochberg false discovery rate (FDR) (23) was applied with a P value <0.05, with 326 genes passing this criterion. The Bonferroni family-wise error rate (FWER) (24,25) was applied with a P value <0.05, with 189 gene qualifiers passing this criterion. Finally, a class prediction using the k-nearest neighbor method (26) was applied to the filtered data to determine which genes had the highest discrimination between normal and RA samples.

Results

Characteristics of the RA patients used in the study, including demographics, disease activity scores, and DMARD use, are illustrated in Table 1. In total, 324 transcripts increased by at least two-fold between the RA and control subjects, and six transcripts decreased by at least two-fold between the RA and control subjects (Table 2).
Table 1

Characteristics of RA patients including demographics, disease activity scores, and DMARD use.

ID

Age, years

Sex

RF titer

Erosions

DMARD use

DAS

RA1

61

F

+

Prednisolone 5 mg/d, methotrexate 15 mg/wk

3.9

RA2

66

F

1/5120

+

Prednisolone 7.5 mg/d, methotrexate 20 mg/wk, sulfasalazine 500 mg BD

4.5

RA3

46

F

1/640

+

Methotrexate 15 mg/wk, hydroxychloroquine 200 mg BD

3.5

RA4

52

F

1/640

Methotrexate 12.5 mg/wk

3.6

RA5

55

F

1/320

+

Methotrexate 12.5 mg/wk, hydroxychloroquine 200 mg BD

3.3

RA6

35

F

1/2560

+

3.0

RA7

74

M

1/320

+

Methotrexate 7.5 mg/wk

3.5

RA8

77

M

1/20400

+

Prednisolone 7.5 mg/d, methotrexate 17.5 mg/wk

3.2

RA 9

49

F

1/1250

+

Methotrexate 10 mg/wk

2.9

Table 2

Differentially regulated transcripts.

Symbol

Name

GenBank acc. no

Map

Freq RA

Freq control

% disease samples, ≥2x or ″−2x

Fold changea

t test (freq)

ANOVA — FDR

ANOVA — FWER

Class predictor gene strength

   

Calcium Binding

       

ANXA11

Annexin A11

L19605

10q23

97.6 ± 9.1

39.1 ± 1.8

89%

2.5 ± 0.2

2.8E–02

1.5E–05

6.0E–04

1.954

S100A4

S100 calcium binding protein A4

M80563

1q21

213.2 ± 19.9

87.6 ± 7.8

89%

2.4 ± 0.2

3.2E–02

5.3E–05

5.3E–03

 

S100A12

S100 calcium binding protein A12

D83657

1q21

65.4 ± 14.0

22.8 ± 4.8

67%

2.6 ± 0.8

5.2E–01

3.3E–03

 

CALM3

Calmodulin 3

J04046

19q13.2–q13.3

29.6 ± 1.8

13.8 ± 1.0

67%

2.1 ± 0.1

6.9E–02

4.7E–06

1.1E–04

 

CACYBP

Calcyclin binding protein

BC001431

1q24–q25

179.2 ± 23.4

72.2 ± 8.3

67%

2.3 ± 0.5

1.1E–01

4.0E–04

 
   

Chaperone

       

HYOU1

Hypoxia up-regulated 1

U65785

11q23.1–q23.3

33.7 ± 3.6

11.4 ± 0.7

78%

3.0 ± 0.3

4.2E–02

2.0E–05

1.1E–03

 

NAP1L4

Nucleosome assembly protein 1-like 4

U77456

11p15.5

26.6 ± 3.6

9.8 ± 0.8

78%

2.7 ± 0.4

5.7E–02

1.9E–04

3.3E–02

 

TTC1

Tetratricopeptide repeat domain 1

U46570

5q32–q33.2

41.7 ± 4.7

16.1 ± 1.3

67%

2.6 ± 0.3

2.9E–02

5.3E–05

5.4E–03

 

DNAJC7

DnaJ (Hsp40) homolog, subfamily C, member 7

U46571

17q11.2

17.8 ± 2.3

6.5 ± 0.5

67%

2.7 ± 0.3

1.6E–01

1.0E–04

1.2E–02

 
   

Cytokine/chemokine

       

IGF2

Insulin growth factor 2 gene, intron 7

S73149

 

34.1 ± 4.9

8.9 ± 0.7

89%

3.8 ± 0.5

8.0E–02

1.9E–05

1.0E–03

1.874

CSF1

Human macrophage-specific colony-stimulating factor

M11296

1p21–p13

28.0 ± 3.6

9.6 ± 0.7

78%

2.9 ± 0.4

9.6E–02

4.3E–05

3.7E–03

 

CCL5

Chemokine (C-C motif) ligand 5

M21121

17q11.2–q12

156.8 ± 14.9

53.7 ± 3.7

78%

2.9 ± 0.3

2.7E–02

2.5E–05

1.5E–03

 

CCL22

Chemokine (C-C motif) ligand 22

U83239

16q13

31.2 ± 5.0

11.2 ± 0.9

67%

2.8 ± 0.4

1.3E–01

4.4E–04

 

CCL22 (duplicate)

Chemokine (C-C motif) ligand 22

U83171

16q13

15.2 ± 2.1

6.2 ± 0.2

67%

2.5 ± 0.3

1.8E–02

6.3E–04

 

TGFB1

Transforming growth factor, β 1

M38449

19q13.2

26.6 ± 4.0

10.1 ± 1.1

67%

2.4 ± 0.6

7.2E–03

1.3E–03

 

MLN

Motilin

X15393

6p21.3

13.4 ± 1.8

6.0 ± 0.4

67%

2.2 ± 0.3

9.5E–02

8.9E–04

 

PF4

Platelet factor 4 (chemokine (C-X-C motif) ligand 4)

M25897

4q12–q21

278.3 ± 14.2

136.5 ± 13.7

56%

2.0 ± 0.1

1.2E–01

1.2E–05

4.7E–04

 

IL7R

Interleukin 7 receptor

M29696

5p13

24.0 ± 10.8

30.2 ± 9.6

67%

−2.3 ± 1.0

1.3E–01

 
   

DNA binding

       

HMGB1

High-mobility group box 1

D63874

13q12

83.2 ± 9.3

27.3 ± 4.3

78%

3.0 ± 0.3

2.5E–01

3.3E–05

2.6E–03

 

MKRN4

Ring zinc-finger protein

U41315

Xp21.1

15.0 ± 1.9

5.8 ± 0.3

67%

2.6 ± 0.3

1.3E–01

3.1E–04

 

HIST2H2AA

Histone 2, H2aa

L19779

1q21.3

71.9 ± 8.2

32.9 ± 3.0

56%

2.2 ± 0.2

5.2E–02

6.6E–05

7.2E–03

 

DDB1

Damage-specific DNA binding protein 1

U32986

1lq12–q13

24.7 ± 3.3

11.0 ± 0.6

67%

2.0 ± 0.5

6.2E–02

1.5E–03

 
   

Enzyme

       

LYZ

Lysozyme

M21119

12q14.3

53.0 ± 27.2

69.2 ± 20.0

67%

−6.6 ± 2.2

8.0E–02

 

AGPAT1

1-acylglycerol-3-phosphate O-acyltransferase 1

U56417

6p21.3

26.3 ± 2.7

7.2 ± 0.4

89%

3.7 ± 0.4

6.6E–02

3.1E–05

2.3E–03

2.006

DIA1

NADH-cytochrome b5 reductase

M28713

 

33.3 ± 3.4

8.9 ± 0.5

100%

3.7 ± 0.4

5.1E–02

2.5E–06

3.7E–05

2.462

KIAA0220

Pl-3-kinase-related kinase SMG-1-like

D86974

16p12.2

239.2 ± 33.3

73.4 ± 8.9

78%

3.3 ± 0.5

1.5E–02

1.2E–04

1.6E–02

 

GSTZ1

Glutathione transferase zeta 1

U86529

14q24.3

25.6 ± 3.3

7.8 ± 0.6

78%

3.3 ± 0.4

1.0E–01

2.5E–05

1.5E–03

 

PYGB

Phosphorylase, glycogen

U47025

20p11.2–p11.1

25.2 ± 2.7

7.8 ± 0.4

89%

3.2 ± 0.3

5.1E–02

1.3E–04

1.9E–02

 

SAT

Spermidine/spermine N1-acetyltransferase

U40369

Xp22.1

37.7 ± 4.0

12.3 ± 2.0

89%

3.1 ± 0.3

4.1E–01

1.9E–05

9.6E–04

 

UROD

Uroporphyrinogen decarboxylase

X89267

1p34

42.7 ± 6.2

14.2 ± 1.1

78%

3.0 ± 0.4

1.1E–01

2.1E–04

3.7E–02

 

GPI

Glucose phosphate isomerase

K03515

19q13.1

35.8 ± 4.5

12.1 ± 1.0

67%

3.0 ± 0.4

2.3E–02

3.3E–05

2.6E–03

 

GSTO1

Glutathione S-transferase omega 1

U90313

10q25.1

43.2 ± 4.2

14.3 ± 1.5

89%

3.0 ± 0.3

8.9E–02

5.4E–06

1.4E–04

 

DDX11

DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11

U75968

12p11

20.6 ± 2.8

7.1 ± 0.6

100%

2.9 ± 0.4

6.3E–02

1.5E–05

6.7E–04

 

IMPDH1

MP (inosine monophosphate) dehydrogenase 1

J05272

7q31.3–q32

31.4 ± 4.7

10.9 ± 0.9

78%

2.9 ± 0.4

3.7E–02

2.3E–04

4.3E–02

 

PIB5PA

Phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A

U45975

22q11.2–q13.2

20.0 ± 2.6

7.2 ± 0.4

67%

2.8 ± 0.4

6.6E–02

2.7E–04

 

CNP

2′,3′-cyclic nucleotide 3′ phosphodiesterase

D13146

17q21

49.9 ± 6.4

17.8 ± 1.4

78%

2.8 ± 0.4

1.3E–01

4.9E–05

4.8E–03

 

UPP1

Uridine Phosphorylase 1

X90858

7p12.3

21.4 ± 1.3

7.6 ± 0.6

89%

2.8 ± 0.2

5.1E–02

2.4E–07

6.1E–07

2.246

AMPD2

Adenosine monophosphate deaminase 2 (isoform L)

M91029

1p13.3

30.3 ± 4.0

11.2 ± 0.8

78%

2.7 ± 0.4

6.6E–02

8.6E–05

9.8E–03

 

BCAT2

Branched chain aminotransferase 2, mitochondrial

U62739

19q13

18.8 ± 2.0

7.1 ± 0.3

78%

2.7 ± 0.3

3.1E–02

1.0E–04

1.2E–02

 

HSD17B3

Hydroxysteroid (17-beta) dehydrogenase 3

U05659

9q22

21.4 ± 2.6

8.1 ± 0.5

78%

2.7 ± 0.3

8.0E–02

1.6E–04

2.5E–02

 

GARS

Glycyl-tRNA synthetase

U09587

7p15

29.7 ± 2.5

11.2 ± 0.7

78%

2.7 ± 0.2

7.6E–02

3.7E–06

7.1E–05

 

PTGS1

Prostaglandin-endoperoxide synthase 1

M59979

9q32–q33.3

14.2 ± 2.3

5.5 ± 0.4

67%

2.6 ± 0.4

7.9E–02

1.6E–03

 

TGM1

Transglutaminase 1

L34840

14q11.2, 3p22–p21.33

18.4 ± 2.3

7.2 ± 0.7

67%

2.6 ± 0.3

1.9E–01

9.2E–05

1.1E–02

 

AOAH

Acyloxyacyl hydrolase

M62840

7p14–p12

25.2 ± 5.4

9.2 ± 0.8

67%

2.5 ± 0.7

2.3E–01

4.8E–03

 

GNPDA1

Glucosamine-6-phosphate deaminase 1

D31766

5q21

13.8 ± 2.0

5.5 ± 0.3

56%

2.5 ± 0.4

6.7E–02

6.4E–04

 

AARS

Alanyl-tRNA synthetase

D32050

16q22

18.1 ± 2.5

7.4 ± 0.3

67%

2.5 ± 0.3

1.6E–01

9.7E–04

 

SETDB1

SET domain, bifurcated 1

D31891

1q21

18.6 ± 2.5

7.4 ± 0.7

67%

2.5 ± 0.3

8.9E–02

1.5E–04

2.3E–02

 

DCTD

Deoxycytidylate deaminase gene

L39874

4q35.1

25.0 ± 3.0

9.8 ± 0.8

67%

2.5 ± 0.3

8.0E–02

5.4E–05

5.5E–03

 

HUMNOSB

Inducible nitric oxide synthase

D29675

 

14.1 ± 2.6

5.3 ± 0.2

67%

2.4 ± 0.6*

2.6E–01

4.1E–03

 

MGLL

Monoglyceride lipase

U67963

3q21.3

18.9 ± 2.0

7.2 ± 0.5

89%

2.4 ± 0.5

9.8E–02

2.3E–04

4.4E–02

 

DAO

D-amino-acid oxidase

D11370

12q24

14.9 ± 2.2

6.2 ± 0.2

56%

2.4 ± 0.4

9.7E–02

1.1E–03

 

DDT

D-dopachrome tautomerase

U49785

22q11.23

24.9 ± 2.9

10.5 ± 0.6

56%

2.4 ± 0.3

4.9E–02

1.1E–04

1.5E–02

 

TPI1

Triosephosphate isomerase 1

M10036

12p13

73.3 ± 8.5

30.0 ± 2.6

78%

2.4 ± 0.3

2.7E–02

1.0E–04

1.3E–02

 

SULT1A3

Sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3

U20499

16p11.2

20.3 ± 2.3

8.3 ± 0.6

67%

2.4 ± 0.3

1.7E–01

7.6E–05

8.5E–03

 

GLA

Galactosidase, alpha

X14448

Xq22

20.6 ± 2.2

8.6 ± 0.9

78%

2.4 ± 0.3

2.8E–01

1.0E–04

1.3E–02

 

PPGB

Protective protein for β-galactosidase

M22960

20q13.1

83.4 ± 8.6

35.2 ± 2.4

78%

2.4 ± 0.2

2.6E–02

4.9E–05

4.8E–03

 

FAH

Fumarylacetoacetate hydrolase

M55150

15q23–q25

18.7 ± 1.1

7.9 ± 0.5

89%

2.4 ± 0.1

4.4E–02

6.8E–07

3.4E–06

2.008

CDA

Cytidine deaminase

L27943

1p36.2–p35

26.9 ± 5.8

10.5 ± 1.0

56%

2.3 ± 0.7

6.4E–02

4.6E–03

 

HYAL2

Hyaluronoglucosaminidase 2

AJ000099

3p21.3

24.9 ± 3.7

10.9 ± 0.8

67%

2.3 ± 0.3

6.4E–02

1.7E–03

 

INPP5D

Inositol polyphosphate-5-phosphatase

U57650

2q36–q37

42.8 ± 5.6

18.8 ± 1.3

67%

2.3 ± 0.3

8.9E–02

4.6E–04

 

CES1

Carboxylesterase 1

L07765

16q13–q22.1

14.0 ± 2.0

6.2 ± 0.2

56%

2.3 ± 0.3

1.0E–01

1.2E–03

 

ACADVL

Acyl-Coenzyme A dehydrogenase

D43682

17p13–p11

41.4 ± 3.8

18.2 ± 1.6

67%

2.3 ± 0.2

2.0E–02

3.2E–05

2.4E–03

 

SULT1A1

Sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1

L19999

16p12.1

21.0 ± 2.3

9.2 ± 1.1

56%

2.3 ± 0.2

2.9E–01

9.3E–05

1.1E–02

 

PRDX6

Peroxiredoxin 6

D14662

1q24.1

36.4 ± 2.7

16.1 ± 2.1

67%

2.3 ± 0.2

1.0E–01

4.4E–05

4.0E–03

 

UQCRC1

Ubiquinol-cytochrome c reductase core protein

L16842

3p21.3

24.1 ± 3.3

10.1 ± 0.8

78%

2.2 ± 0.5

7.5E–02

5.4E–04

 

GUSB

Glucuronidase, beta

M15182

7q21.11

18.9 ± 2.2

8.5 ± 0.5

56%

2.2 ± 0.3

4.9E–02

1.2E–04

1.6E–02

 

HK3

Hexokinase 3

U51333

5q35.2

47.1 ± 7.3

20.0 ± 2.0

56%

2.1 ± 0.5

3.4E–01

1.6E–03

 

CHKL

Choline kinase-like

U62317

22q13.33

60.8 ± 7.0

26.6 ± 1.5

67%

2.1 ± 0.4

1.1E–01

5.0E–04

 

PGM1

Phosphoglucomutase 1

M83088

1p31

16.7 ± 1.5

7.8 ± 0.5

56%

2.1 ± 0.2

2.4E–01

4.6E–05

4.2E–03

 

PCSK6

Proprotein convertase subtilisin/kexin type 6

M80482

15q26

10.7 ± 1.1

5.1 ± 0.1

44%

2.1 ± 0.2

3.7E–02

1.7E–04

2.6E–02

 

PMM1

Phosphomannomutase 1

U86070

22q13.2

13.8 ± 1.3

6.6 ± 0.2

56%

2.1 ± 0.2

3.6E–02

1.7E–04

2.7E–02

 

TALDO1

Transaldolase 1

L19437

11p15.5–p15.4

85.3 ± 9.9

37.7 ± 3.0

78%

2.0 ± 0.5

1.2E–01

6.4E–04

 
   

Extracellular matrix

       

EPB49

Erythrocyte membrane protein band 4.9 (dematin)

L19713

8p21.1

38.7 ± 4.3

9.9 ± 0.8

100%

3.9 ± 0.4

2.8E–02

3.1E–06

5.2E–05

2.064

SPARC

Secreted protein, acidic, cysteine-rich (osteonectin)

J03040

5q31.3–q32

57.8 ± 8.2

24.4 ± 3.5

56%

2.4 ± 0.3

1.1E–01

4.0E–04

 
   

Integral intracellular membrane

       

CPT1B

Carnitine palmitoyltransferase 1B (muscle)

Y08682

22q13.33

13.6 ± 1.9

4.9 ± 0.2

67%

2.8 ± 0.4

8.0E–02

3.3E–04

 

STX5A

Syntaxin 5A

U26648

11q12.3

19.9 ± 2.2

7.9 ± 0.6

89%

2.5 ± 0.3

1.8E–02

1.9E–05

9.0E–04

 

HAX1

HS1 binding protein

U68566

1q22

31.0 ± 2.9

13.9 ± 1.2

67%

2.2 ± 0.2

7.7E–02

4.9E–05

4.6E–03

 

BAP1

BRCA1 associated protein-1

D87462

3p21.31–p21.2

12.9 ± 1.0

6.2 ± 0.3

56%

2.1 ± 0.2

1.4E–02

5.4E–05

5.6E–03

 

BZRP

Benzodiazapine receptor (peripheral)

L21954

22q13.31

127.9 ± 26.1

50.5 ± 4.3

56%

2.3 ± 0.6

1.9E–01

4.8E–03

 

BCL2

B-cell CLL/lymphoma 2

M14745

18q21.33

16.2 ± 2.1

7.5 ± 0.6

44%

1.9 ± 0.5

1.4E–01

8.0E–04

 

HERPUD1

Homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1

D14695

16q12.2–q13

16.6 ± 3.1

7.0 ± 0.6

56%

1.9 ± 0.7

4.2E–01

7.8E–03

 
   

Integral plasma membrane

       

STAB1

Stabilin 1

D87433

3p21.31

30.2 ± 6.7

4.7 ± 0.2

100%

6.4 ± 1.4*

1.8E–01

6.3E–05

6.8E–03

2.164

IGHG3

Immunoglobulin heavy constant γ 3

M87789

14q32.33

105.6 ± 38.7

15.8 ± 2.5

67%

6.3 ± 2.6

1.2E–01

1.4E–02

 

ZYX

Zyxin

X95735

7q32

38.0 ± 6.5

10.5 ± 1.0

78%

3.6 ± 0.6

4.1E–02

4.7E–04

 

SELPLG

Selectin P ligand

U25956

12q24

75.9 ± 10.0

21.1 ± 1.8

78%

3.6 ± 0.5

4.4E–02

2.2E–05

1.3E–03

 

PRF1

Perforin

M31951

10q22

16.9 ± 6.6

25.0 ± 3.8

67%

−3.4 ± 1.2

1.0E + 00

 

CD151

CD151 antigen

D29963

11p15.5

29.2 ± 4.9

8.7 ± 0.8

78%

3.4 ± 0.6

2.9E–01

1.3E–04

1.8E–02

 

CD63

CD63 antigen

X62654

12q12–q13

41.8 ± 6.7

12.4 ± 1.3

89%

3.4 ± 0.5

1.4E–01

1.0E–04

1.2E–02

 

IFNGR2

Interferon γ receptor 2

U05875

21q22.11

37.9 ± 6.9

11.5 ± 1.1

56%

3.3 ± 0.6

1.3E–01

3.4E–04

 

TRIP12

Thyroid hormone receptor interactor 12

D28476

2q37.1

27.4 ± 3.7

8.9 ± 1.0

78%

3.1 ± 0.4

2.4E–01

1.4E–04

2.1E–02

 

LENG4

Leukocyte receptor cluster member 4

S82470

19q13.4

26.8 ± 3.9

8.7 ± 0.6

78%

3.1 ± 0.4

8.6E–02

1.6E–04

2.5E–02

 

CSF3R

Colony stimulating factor 3 receptor

M59820

1p35–p34.3

33.3 ± 6.9

10.2 ± 0.8

67%

3.0 ± 0.8

5.9E–02

4.2E–03

 

GP1BB

Glycoprotein lb (platelet), β polypeptide

U59632

22q11.21

97.2 ± 16.2

30.5 ± 3.3

67%

3.0 ± 0.7

6.9E–02

7.1E–04

 

FLOT2

Flotillin 2

M60922

17q11–q12

50.4 ± 7.9

16.1 ± 1.2

78%

2.8 ± 0.7

2.8E–02

3.9E–03

 

VAT1

Vesicle amine transport protein 1 homolog

U18009

17q21

12.3 ± 1.2

4.5 ± 0.1

78%

2.8 ± 0.3*

1.1E–01

2.5E–05

1.6E–03

2.327

MCL1

Myeloid cell leukemia sequence 1

L08246

1q21

88.7 ± 9.7

32.2 ± 3.9

78%

2.8 ± 0.3

6.6E–02

5.7E–05

6.0E–03

 

HIA-DQA1

Major histocompatibility complex, class II, DQα 1

M34996

6p21.3

80.6 ± 18.7

25.1 ± 3.7

56%

2.7 ± 1.0

2.2E–01

6.8E–03

 

MICB

MHC class I chain-related gene B

U65416

6p21.3

17.3 ± 2.1

6.5 ± 0.2

67%

2.7 ± 0.3

1.2E–01

2.0E–04

3.5E–02

 

CD7

CD7 antigen

D00749

17q25.2–q25.3

69.9 ± 8.8

25.8 ± 2.1

67%

2.7 ± 0.3

4.3E–03

1.7E–04

2.9E–02

 

LILRA2

Leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2

U82275

19q13.4

25.4 ± 4.7

8.8 ± 0.8

67%

2.6 ± 0.7

1.4E–01

2.1E–03

 

HEM1

Hematopoietic protein 1

M58285

12q13.1

38.4 ± 5.1

14.6 ± 2.0

67%

2.6 ± 0.3

1.2E–01

1.7E–04

2.7E–02

 

FCGRT

Fc fragment of IgG, receptor, transporter, alpha

U12255

19q13.3

78.6 ± 13.7

29.2 ± 2.5

67%

2.5 ± 0.6

1.1E–01

2.8E–03

 

SPG7

Spastic paraplegia 7 homolog

X65784

16q24.3

21.6 ± 2.2

8.5 ± 0.5

78%

2.5 ± 0.3

6.4E–02

3.2E–05

2.4E–03

 

IL10RB

Interleukin 10 receptor, beta

Z17227

21q22.1–q22.2

15.8 ± 1.6

6.2 ± 0.4

78%

2.5 ± 0.3

3.7E–02

3.6E–05

2.9E–03

 

SELF

Selectin P

M25322

1q22–q25

15.0 ± 1.2

5.9 ± 0.4

78%

2.5 ± 0.2

1.0E–01

1.5E–06

1.4E–05

2.018

CEACAM4

Carcinoembryonic antigen-related cell adhesion molecule 4

D90276

19q13.2

13.3 ± 2.1

5.5 ± 0.2

56%

2.4 ± 0.4*

5.8E–02

1.7E–03

 

CD3E

CD3E antigen, epsilon polypeptide

M23323

11q23

45.8 ± 5.8

18.9 ± 1.0

67%

2.4 ± 0.3

4.0E–02

4.0E–04

 

AAMP

Angio-associated, migratory cell protein

M95627

2q35

22.1 ± 3.2

9.4 ± 0.7

56%

2.4 ± 0.3

5.1E–02

1.1E–03

 

LAMP1

Lysosomal-associated membrane protein 1

J04182

13q34

47.8 ± 4.5

20.2 ± 2.0

67%

2.4 ± 0.2

7.4E–02

3.3E–05

2.6E–03

 

BST2

Bone marrow stromal cell antigen 2

D28137

19p13.2

46.3 ± 9.5

16.4 ± 1.6

78%

2.3 ± 0.8

2.5E–01

9.3E–03

 

CD33

CD33 antigen

M23197

19q13.3

19.4 ± 3.1

7.6 ± 0.7

56%

2.3 ± 0.5

2.3E–01

1.3E–03

 

ACRV1

Intra-acrosomal protein

S65583

11p12–q13

12.8 ± 2.3

5.5 ± 0.2

56%

2.3 ± 0.4*

7.3E–02

2.9E–03

 

PTTG1IP

Pituitary tumor-transforming 1 interacting protein

Z50022

21q22.3

30.0 ± 3.3

13.0 ± 0.9

56%

2.3 ± 0.3

6.0E–02

1.7E–04

2.7E–02

 

HDLBP

High density lipoprotein binding protein (vigilin)

M64098

2q37

18.8 ± 2.3

8.3 ± 0.6

67%

2.3 ± 0.3

5.3E–02

2.9E–04

 

ICAM3

Intercellular adhesion molecule 3

X69819

19p13.3–p13.2

52.2 ± 4.4

22.6 ± 1.7

67%

2.3 ± 0.2

8.2E–03

2.0E–05

1.1E–03

 

OS-9

Amplified in osteosarcoma

U41635

12q13

58.6 ± 7.7

24.2 ± 1.8

67%

2.2 ± 0.5

8.3E–02

9.9E–04

 

EMP3

Epithelial membrane protein 3

U52101

19q13.3

159.3 ± 21.9

65.2 ± 4.9

67%

2.2 ± 0.5

1.5E–03

1.1E–03

 

HA-1

Minor histocompatibility antigen HA-1

D86976

19p13.3

103.1 ± 11.3

43.5 ± 2.0

78%

2.2 ± 0.4

3.5E–02

1.7E–04

2.8E–02

 

EBI3

Epstein-Barr virus induced gene 3

L08187

19p13.3

12.8 ± 1.7

5.8 ± 0.2

56%

2.2 ± 0.3

3.1E–02

5.4E–04

 

SPN

Sialophorin

M61827

16p11.2

33.2 ± 4.5

15.0 ± 1.3

67%

2.2 ± 0.3

8.3E–02

6.9E–04

 

CD19

CD19 antigen

M84371

16p11.2

14.6 ± 1.3

6.7 ± 0.3

67%

2.2 ± 0.2

1.0E–02

1.1E–04

1.5E–02

 

ITGAX

Integrin, α X

M81695

16p11.2

32.2 ± 4.8

13.8 ± 1.0

44%

2.1 ± 0.5

2.1E–01

1.1E–03

 

P2RX5

Purinergic receptor P2X, ligand-gated ion channel, 5

U49395

17p13.3

17.4 ± 1.8

8.2 ± 0.7

56%

2.1 ± 0.2

3.1E–02

1.7 E–04

2.8E–02

 

HLA-DOA

Major histocompatibility complex, class II, DO alpha

M31525

6p21.3

13.6 ± 1.6

6.4 ± 0.4

56%

2.1 ± 0.2

7.8E–02

3.5E–04

 

KLRK1

Killer cell lectin-like receptor subfamily K, member 1

X54870

12p13.2–p12.3

31.3 ± 3.8

13.4 ± 1.5

67%

2.0 ± 0.5

1.2E–03

6.8E–04

 

ITGB2

Integrin, β 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1

M15395

21q22.3

86.1 ± 7.9

37.8 ± 3.9

78%

2.0 ± 0.4

1.2E–01

1.8E–04

3.1E–02

 

LAPTM5

Lysosomal-associated multispanning membrane protein-5

U51240

1p34

146.9 ± 21.8

61.8 ± 5.4

67%

1.9 ± 0.6

1.2E–01

2.8E–03

 
   

Mitochondrial

       

UCP2

Uncoupling protein 2

U94592

11

50.2 ± 6.6

22.5 ± 2.0

56%

2.0 ± 0.5

4.8E–03

7.9E–04

 
   

Other

       

IER2

Immediate early response 2

M62831

19p13.13

105.7 ± 17.3

28.7 ± 1.7

78%

3.5 ± 0.7

6.4E–02

3.7E–04

 

PTMA

Prothymosin, alpha

M14483

2q35–q36

65.9 ± 17.1

109.3 ± 8.0

44%

−3.4 ± 1.5

9.7E–01

3.9E–02

 

CRIP2

Cysteine-rich protein 2

D42123

14q32.3

25.6 ± 3.2

8.1 ± 0.6

78%

3.2 ± 0.4

1.5E–01

1.1E–04

1.4E–02

 

PHC2

Polyhomeotic-like 2

U89278

1p34.3

23.4 ± 3.0

7.8 ± 0.3

89%

3.0 ± 0.4

6.3E–02

1.7E–04

2.7E–02

 

FTH1

Ferritin, heavy polypeptide 1

L20941

11q13

279.0 ± 16.1

122.8 ± 5.7

67%

2.3 ± 0.1

2.9E–02

2.4E–07

7.2E–07

2.452

PFC

Properdin P factor, complement

M83652

Xp11.3–p11.23

46.6 ± 8.4

19.1 ± 1.8

56%

2.2 ± 0.6

1.8E–01

1.2E–02

 

IFI44

Interferon-induced protein 44

D28915

1p31.1

13.6 ± 2.5

5.5 ± 0.3

56%

2.0 ± 0.7

7.2E–01

5.5E–03

 
   

Proteases or inhibitors

       

PCOLN3

Procollagen (type III) N-endopeptidase

U58048

16q24.3

17.3 ± 2.3

5.4 ± 0.2

78%

3.2 ± 0.4

8.0E–02

1.4E–04

2.0E–02

 

MME

Membrane metallo-endopeptidase

J03779

3q25.1–q25.2

24.6 ± 3.4

7.8 ± 0.7

67%

3.1 ± 0.4

2.2E–01

1.9E–04

3.1E–02

 

ADAM8

A disintegrin and metalloproteinase domain 8

D26579

10q26.3

31.6 ± 4.1

10.6 ± 0.9

67%

3.0 ± 0.4

6.7E–02

4.9E–05

4.5E–03

 

SERPINB6

Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6

S69272

6p25

24.7 ± 2.8

8.7 ± 0.5

89%

2.8 ± 0.3

3.0E–02

1.9E–05

9.5E–04

 

TIMP2

Tissue inhibitor of metalloproteinase 2

M32304

17q25

25.7 ± 3.3

8.8 ± 0.8

78%

2.7 ± 0.5

6.2E–02

2.0E–04

3.3E–02

 

CTSD

Cathepsin D

M63138

11p15.5

82.9 ± 16.7

30.3 ± 2.0

56%

2.7 ± 0.6

6.4E–02

1.0E–03

 

SPINT2

Serine protease inhibitor, Kunitz type, 2

U78095

19q13.1

23.9 ± 1.9

10.5 ± 0.9

89%

2.3 ± 0.2

1.0E–01

7.2E–06

2.1E–04

 

NOMO1

PM5 protein, centromeric copy

X57398

16p13.11

27.3 ± 2.9

11.5 ± 0.9

78%

2.4 ± 0.2

5.6E–02

1.2E–04

1.5E–02

 

PSME1

Proteasome (prosome, macropain) activator subunit 1

L07633

14q11.2

84.3 ± 11.3

34.9 ± 3.2

56%

2.2 ± 0.5

1.1E–01

5.5E–04

 

PSMD2

Proteasome 26S subunit, non-ATPase, 2

D78151

3q27.3

36.2 ± 4.5

16.0 ± 1.2

56%

2.3 ± 0.3

1.3E–01

2.1 E–04

3.7E–02

 

CTSB

Cathepsin B

M14221

8p22

71.3 ± 11.1

29.8 ± 2.8

56%

2.1 ± 0.6

2.2E–01

6.6E–03

 

PSMA4

Proteasome subunit, a type, 4

D00763

15q24.1

42.8 ± 5.9

17.8 ± 2.6

67%

2.2 ± 0.5

2.9E–01

5.7E–04

 
   

Ribosomal

       

MRPL28

Mitochondrial ribosomal protein L28

U19796

16p13.3

22.0 ± 2.7

6.2 ± 0.3

100%

3.5 ± 0.4

1.2E–01

6.2E–06

1.7E–04

2.299

RPL39

Ribosomal protein L39

D79205

Xq22–q24

465.1 ± 21.5

226.3 ± 24.3

22%

2.1 ± 0.1

1.3E–01

1.9E–05

8.7E–04

 

RPS4Y1

Ribosomal protein S4, Y-linked 1

M58459

Yp11.3

15.1 ± 7.7

32.2 ± 6.4

78%

−5.5 ± 1.4

9.7E–01

 
   

Signal transduction

       

CSRP1

Cysteine and glycine-rich protein 1

M76378

1q32

21.0 ± 2.7

5.7 ± 0.4

89%

3.7 ± 0.5

1.3E–01

2.9E–05

2.0E–03

1.937

GNAZ

Guanine nucleotide binding protein (G protein), α z polypeptide

J03260

22q 11.22

24.9 ± 3.9

7.6 ± 0.5

67%

3.3 ± 0.5

1.0E–01

2.1 E–04

3.6E–02

 

CDC25B

Cell division cycle 25B

S78187

20p13

63.9 ± 8.5

19.1 ± 1.5

89%

3.3 ± 0.4

8.5E–02

5.6E–05

5.9E–03

 

ILK

Integrin-linked kinase

U40282

11p15.5–p15.4

29.2 ± 4.1

8.3 ± 0.7

78%

3.3 ± 0.7

5.6E–02

2.8E–04

 

PTPRN

Protein tyrosine phosphatase, receptor type, N

L18983

2q35–q36.1

20.8 ± 2.9

6.4 ± 0.4

78%

3.3 ± 0.5

9.5E–02

1.1E–04

1.4E–02

 

TSC2

Tuberous sclerosis 2

L48546

16p13.3

30.4 ± 3.3

9.2 ± 0.6

78%

3.3 ± 0.4

3.8E–02

1.2E–05

4.3E–04

1.984

BRD2

Bromodomain containing 2

X62083

6p21.3

70.9 ± 8.0

21.2 ± 2.8

78%

3.4 ± 0.4

1.2E–01

1.9E–05

9.8E–04

 

CLU

Clusterin

M63379

8p21–p12

222.8 ± 26.1

72.8 ± 6.8

78%

3.1 ± 0.4

3.6E–02

1.6E–05

7.2E–04

 

INPP5E

Inositol polyphosphate-5-phosphatase

U45974

9q34.3

15.1 ± 1.3

4.7 ± 0.2

89%

3.2 ± 0.3*

1.1E–01

3.9E–06

8.9E–05

2.575

LTK

Leukocyte tyrosine kinase

D16105

15q15.1–q21.1

23.8 ± 3.2

7.2 ± 0.8

89%

3.3 ± 0.4

4.1E–01

2.1E–05

1.2E–03

 

NRGN

Neurogranin

X99076

11q24

230.1 ± 27.2

76.5 ± 7.2

78%

3.0 ± 0.4

3.4E–02

2.5E–05

1.6E–03

 

PLCB2

Phospholipase C, β 2

M95678

15q15

84.0 ± 7.8

25.6 ± 1.9

100%

3.3 ± 0.3

1.9E–02

6.4E–07

2.6E–06

2.064

PKM2

Pyruvate kinase, muscle

X56494

15q22

60.0 ± 6.5

18.8 ± 1.5

78%

3.2 ± 0.3

1.3E–02

7.2E–06

2.2E–04

 

PSD

Pleckstrin and Sec7 domain containing

X99688

10q24

23.4 ± 3.7

7.8 ± 0.6

67%

3.0 ± 0.5

2.0E–01

2.8E–04

 

MAP2K3

Mitogen-activated protein kinase kinase 3

D87116

17q11.2

32.9 ± 4.1

11.2 ± 1.1

78%

2.9 ± 0.4

8.5E–02

4.9E–05

4.6E–03

 

IKBKE

Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon

D63485

1q32.1

18.9 ± 2.1

6.7 ± 0.4

78%

2.8 ± 0.3

1.2E–01

1.4E–04

2.0E–02

 

FASTK

FAST kinase

X86779

7q35

20.3 ± 2.4

7.0 ± 0.5

78%

2.9 ± 0.3

2.8E–02

8.5E–05

9.7E–03

 

LSP1

Lymphocyte-specific protein 1

M33552

11p15.5

48.1 ± 7.2

15.9 ± 1.8

78%

3.0 ± 0.5

4.5E–04

6.9E–05

7.5E–03

 

RABGGTA

Rab geranylgeranyltransferase, α subunit

Y08200

14q11.2

23.6 ± 3.1

8.6 ± 0.5

67%

2.7 ± 0.4

5.4E–02

1.4E–04

2.1E–02

 

MADD

MAP-kinase activating death domain

AB002356

11p11.2

31.7 ± 4.1

11.2 ± 0.7

67%

2.8 ± 0.4

1.5E–01

1.0E–04

1.3E–02

 

CSNK2A2

Casein kinase 2, α prime polypeptide

M55268

16p13.3–p13.2

17.3 ± 1.8

6.1 ± 0.2

78%

2.9 ± 0.3

1.7E–01

4.3E–05

3.8E–03

2.056

CCND3

Cyclin D3

M92287

6p21

68.3 ± 6.2

23.6 ± 2.3

78%

2.9 ± 0.3

5.0E–02

3.9E–06

8.5E–05

 

CENTB1

Centaurin, β 1

D30758

17p13.2

61.9 ± 6.3

22.6 ± 1.7

67%

2.7 ± 0.3

1.2E–02

2.5E–05

1.6E–03

 

PRKACG

Protein kinase, cAMP-dependent, catalytic, γ

M34182

9q13

41.6 ± 3.1

15.1 ± 1.5

89%

2.8 ± 0.2

1.2E–02

1.7E–06

2.2E–05

 

YWHAH

Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide

D78577

22q12.3

85.7 ± 5.7

31.1 ± 4.3

89%

2.8 ± 0.2

8.9E–02

2.8E–05

1.9E–03

 

NCF1

Neutrophil cytosolic factor 1

M55067

7q11.23

72.3 ± 13.7

22.1 ± 1.7

78%

3.1 ± 0.8

1.3E–02

1.2E–03

 

ARHGEF2

Rho/rac guanine nucleotide exchange factor 2

U72206

1q21–q22

25.6 ± 5.7

8.7 ± 0.7

56%

2.7 ± 0.8

2.9E–02

8.8E–03

 

TRAF1

TNF receptor-associated factor 1

U19261

9q33–q34

20.4 ± 2.6

7.3 ± 0.3

78%

2.6 ± 0.5

1.0E–01

3.4E–04

 

TRAF4

TNF receptor-associated factor 4

X80200

17q11–q12

15.1 ± 2.2

6.0 ± 0.3

56%

2.5 ± 0.4

6.0E–02

4.6E–04

 

ARAF1

V-raf murine sarcoma 3611 viral oncogene homolog

U01337

Xp11.4–p11.2

32.7 ± 2.8

11.8 ± 0.9

89%

2.8 ± 0.2

1.6E–02

1.6E–06

1.7E–05

 

CSK

C-src tyrosine kinase

X59932

15q23–q25

62.4 ± 8.0

22.5 ± 1.6

78%

2.8 ± 0.4

9.4E–03

1.2E–04

1.6E–02

 

FKBP4

FK506 binding protein 4, 59kDa

M88279

12p13.33

23.1 ± 3.2

8.8 ± 0.4

67%

2.6 ± 0.4

4.8E–02

4.8E–04

 

GNG10

Guanine nucleotide binding protein (G protein), γ 10

U31383

9q32

18.3 ± 3.0

6.7 ± 0.7

56%

2.7 ± 0.4

2.8E–01

3.7E–04

 

TNFRSF14

Tumor necrosis factor receptor superfamily, member 14

U70321

1p36.3–p36.2

28.1 ± 2.6

10.5 ± 0.7

78%

2.7 ± 0.2

7.5E–03

5.4E–06

1.4E–04

 

ARHGEF16

Rho guanine exchange factor 16

D89016

1p36.3

18.8 ± 3.0

6.6 ± 0.4

67%

2.6 ± 0.6

3.4E–01

2.9E–03

 

TNFRSF1B

Tumor necrosis factor receptor superfamily, member 1B

M32315

1p36.3–p36.2

67.4 ± 11.4

24.6 ± 2.6

67%

2.7 ± 0.5

4.9E–02

2.6E–04

4.9E–02

 

PIM1

Pim-1 oncogene

M16750

6p21.2

34.9 ± 4.5

13.9 ± 1.1

67%

2.3 ± 0.5

1.0E–01

6.0E–04

 

STK19

Serine/threonine kinase 19

BC016916

6p21.3

12.8 ± 1.5

5.4 ± 0.3

78%

2.4 ± 0.3*

4.3E–02

1.7E–04

2.8E–02

 

NDRG1

N-myc downstream regulated gene 1

D87953

8q24.3

39.6 ± 5.4

15.5 ± 1.1

67%

2.6 ± 0.3

1.3E–01

4.7E–04

 

PXN

Paxillin

U14588

12q24

39.1 ± 3.1

15.3 ± 1.8

89%

2.6 ± 0.2

4.2E–02

1.5E–05

6.7E–04

 

IHPK1

Inositol hexaphosphate kinase 1

D87452

3p21.31

14.1 ± 1.4

5.6 ± 0.2

67%

2.5 ± 0.2

2.4E–02

1.0E–04

1.3E–02

 

STAT5A

Signal transducer and activator of transcription 5A

U43185

17q11.2

27.6 ± 4.3

10.4 ± 0.8

78%

2.7 ± 0.4

5.4E–02

2.8E–04

 

SQSTM1

Sequestosome 1

U46751

5q35

98.8 ± 10.3

40.8 ± 2.5

67%

2.4 ± 0.3

1.6E–02

4.6E–05

4.1E–03

 

HDGF

Hepatoma-derived growth factor

BCO18991

X

41.6 ± 5.0

17.3 ± 1.6

67%

2.4 ± 0.3

8.6E–02

2.1E–04

3.7E–02

 

MPP1

Membrane protein, palmitoylated 1

M64925

Xq28

34,9 ± 4.9

15.5 ± 2.1

67%

2.2 ± 0.3

7.4E–01

7.1E–04

 

RGL2

Ral guanine nucleotide dissociation stimulator-like 2

U68142

6p21.3

15.7 ± 1.2

6.6 ± 0.3

78%

2.4 ± 0.2

4.5E–02

9.1E–06

3.1E–04

2.042

MX1

Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78

M33882

21q22.3

30.1 ± 8.8

8.7 ± 1.0

67%

3.0 ± 1.2

9.3E–01

1.4E–02

 

RPS6KA1

Ribosomal protein S6 kinase, 90kDa, polypeptide 1

L07597

3

28.8 ± 4.3

11.3 ± 1.1

67%

2.5 ± 0.4

1.2E–01

1.3E–04

1.8E–02

 

ITPK1

Inositol 1,3,4-triphosphate 5/6 kinase

U51336

14q31

49.0 ± 6.3

20.2 ± 1.4

56%

2.4 ± 0.3

5.7E–02

1.5E–04

2.2E–02

 

ARF3

ADP-ribosylation factor 3

M74491

12q13

54.1 ± 5.9

23.2 ± 2.7

56%

2.3 ± 0.3

5.7E–02

1.6E–04

2.4E–02

 

FKBP1A

FK506 binding protein 1A

M34539

20p13

42.8 ± 5.0

17.5 ± 1.3

67%

2.4 ± 0.3

1.9E–02

1.1E–04

1.4E–02

 

PRKAG1

Protein kinase, AMP-activated, γ 1 non-catalytic subunit

U42412

12q12–q14

15.4 ± 2.0

6.7 ± 0.3

67%

2.3 ± 0.3

5.4E–02

1.4E–03

 

BIRC1

Baculoviral IAP repeat-containing 1

U80017

5q12.2–q13.3

12.5 ± 1.5

5.8 ± 0.3

44%

2.1 ± 0.3

7.5E–02

2.3E–04

4.1E–02

 

ARHGEF1

Rho guanine nucleotide exchange factor 1

U64105

19q13.13

43.6 ± 3.7

19.2 ± 1.4

67%

2.3 ± 0.2

1.0E–02

1.5E–05

6.0E–04

 

AVPR1B

Arginine vasopressin receptor 1B

L37112

1q32

14.3 ± 1.4

6.4 ± 0.4

56%

2.2 ± 0.2

1.1E–01

5.8E–05

6.2E–3

 

DGKZ

Diacylglycerol kinase, zeta

U51477

11p11.2

32.6 ± 2.9

13.8 ± 0.8

67%

2.4 ± 0.2

2.8E–02

9.1E–06

3.2E–04

 

PARK7

Parkinson disease (autosomal recessive, early onset) 7

D61380

1p36.33–p36.12

58.4 ± 5.9

26.2 ± 3.0

56%

2.2 ± 0.2

1.3E–01

1.8E–04

2.9E–02

 

RGS2

G0/G1 switch regulatory gene # 8

L13391

1q31

60.3 ± 12.5

21.4 ± 3.2

67%

2.3 ± 0.8

2.7E–01

8.1E–03

 

PPM IF

Protein phosphatase 1F (PP2C domain containing)

D13640

22q11.22

29.0 ± 4.3

11.2 ± 1.0

67%

2.4 ± 0.6

1.7E–01

1.3E–03

 

ARF5

ADP-ribosylation factor 5

M57567

7q31.3

42.4 ± 6.2

16.2 ± 1.4

78%

2.4 ± 0.5

5.1E–02

4.0E–04

 

PTK2B

PTK2B protein tyrosine kinase 2 beta

U43522

8p21.1

13.2 ± 2.2

5.8 ± 0.3

56%

2.3 ± 0.4

5.0E–03

1.5E–03

 

PIM1

Pim-1 oncogene

M54915

6p21.2

54.7 ± 6.4

23.5 ± 1.8

78%

2.1 ± 0.4

1.1E–01

3.4E–04

 

INPPL1

Inositol polyphosphate phosphatase-like 1

L36818

11q23

19.4 ± 2.8

8.2 ± 0.9

56%

2.4 ± 0.3

1.3E–01

2.1E–04

3.8E–02

 

PCMT1

Protein-L-isoaspartate (D-aspartate) O-methyltransferase

D25547

6q24–q25

13.2 ± 2.3

5.8 ± 0.2

44%

2.3 ± 0.4

1.3E–01

1.4E–03

 

ARHGAP1

Rho GTPase activating protein 1

U02570

11p12–q12

25.6 ± 3.3

11.8 ± 0.8

56%

2.2 ± 0.3

3.4E–02

6.9E–04

 

FKBP2

FK506 binding protein 2, 13kDa

M75099

11q13.1–q13.3

23.6 ± 3.1

10.8 ± 0.9

56%

2.2 ± 0.3

7.0E–02

9.7E–04

 

TNIP1

TNFAIP3 interacting protein 1

D30755

5q32–q33.1

29.1 ± 4.0

12.8 ± 0.9

56%

2.3 ± 0.3

5.0E–02

2.2E–04

4.0E–02

 

IRAK1

Interleukin-1 receptor-associated kinase 1

L76191

Xq28

32.7 ± 2.8

15.5 ± 1.1

56%

2.1 ± 0.2

8.1E–02

2.0E–05

1.0E–03

 

RHOG

Ras homolog gene family, member G (rho G)

X61587

11p15.5–p15.4

51.9 ± 8.5

19.7 ± 1.6

78%

2.2 ± 0.7

8.0E–03

4.4E–03

 

RASSF2

Ras association (RalGDS/AF-6) domain family 2

D79990

20pter–p12.1

29.3 ± 4.5

12.3 ± 1.7

56%

2.1 ± 0.6

4.3E–01

3.7E–03

 

NEDD8

Neural precursor cell expressed, developmentally down-regulated 8

D23662

14q11.2

53.1 ± 6.8

23.8 ± 2.6

67%

2.0 ± 0.5

1.9E–01

8.6E–04

 

CAP1

CAP, adenylate cyclase-associated protein 1

L12168

1p34.2

134.7 ± 18.9

58.4 ± 5.4

67%

2.1 ± 0.5

4.2E–02

3.1E–03

 

ZAP70

Zeta-chain (TCR) associated protein kinase

L05148

2q12

36.6 ± 4.3

16.3 ± 1.4

78%

2.0 ± 0.4

4.4E–02

5.1E–04

 

FKBP8

FK506 binding protein 8

L37033

19p12

27.4 ± 3.7

12.3 ± 1.1

56%

2.0 ± 0.5

1.4E–02

7.6E–04

 

GRK6

G protein-coupled receptor kinase 6

L16862

5q35

23.4 ± 3.6

10.5 ± 1.0

56%

2.0 ± 0.5

3.0E–02

1.3E–03

 

MAP2K2

Mitogen-activated protein kinase kinase 2

L11285

7q32

29.1 ± 4.0

12.9 ± 0.7

67%

2.0 ± 0.5

1.5E–02

1.3E–03

 

PTP4A2

Protein tyrosine phosphatase type IVA, member 2

U14603

1p35

76.6 ± 9.4

35.3 ± 2.6

56%

1.9 ± 0.4

2.0E–02

5.7E–04

 

RAC1

Ras-related C3 botulinum toxin substrate 1

NM_006908

7p22

20.1 ± 3.4

8.9 ± 0.6

56%

2.0 ± 0.5

3.4E–02

3.2E–03

 

MX2

Myxovirus (influenza virus) resistance 2

M30818

21q22.3

20.6 ± 3.9

8.7 ± 0.9

56%

1.9 ± 0.7

7.0E–01

8.6E–03

 

FYB

FYN binding protein (FYB-120/130)

U93049

5p13.1

5.2 ± 0.7

10.8 ± 1.9

67%

−2.3 ± 0.2

4.3E–01

7.1E–03

 
   

Structural

       

MYL9

Myosin, light polypeptide 9, regulatory

J02854

20q 11.23

17.9 ± 4.7

4.4 ± 0.2

67%

4.1 ± 1.1*

1.4E–01

1.1E–03

 

PLEC1

Plectin 1, intermediate filament binding protein

U53204

8q24

37.8 ± 6.0

9.6 ± 0.9

78%

3.9 ± 0.6

3.0E–02

3.4E–05

2.8E–03

 

GFAP

Glial fibrillary acidic protein

S40719

17q21

19.9 ± 3.2

7.2 ± 0.5

67%

2.8 ± 0.4

1.9E–01

3.5E–04

 

BECN1

Beclin 1

L38932

17q21

40.3 ± 4.0

14.8 ± 1.2

78%

2.7 ± 0.3

5.7E–02

1.6E–05

7.4E–04

 

MYH9

Myosin, heavy polypeptide 9, non-muscle

M31013

22q13.1

149.8 ± 13.7

55.4 ± 4.4

78%

2.7 ± 0.2

5.8E–02

6.7E–06

1.9E–04

 

KRT1

Keratin 1

M98776

12q12–q13

16.7 ± 2.9

6.2 ± 0.3

67%

2.5 ± 0.6

4.9E–01

3.0E–03

 

NUMA1

Nuclear mitotic apparatus protein 1

Z14227

11q13

25.7 ± 3.4

9.5 ± 0.6

78%

2.7 ± 0.4

5.5E–02

3.4E–04

 

PDLIM1

PDZ and UM domain 1 (elfin)

U90878

10q22–q26.3

26.6 ± 2.9

11.0 ± 0.8

56%

2.4 ± 0.3

3.6E–02

2.5E–05

1.6E–03

 

MYL6

Myosin, light polypeptide 6, alkali, smooth muscle and non-muscle

M31212

12

360.2 ± 18.0

138.0 ± 13.6

89%

2.6 ± 0.1

2.4E–02

3.9E–06

8.1E–05

 

SAFB

Scaffold attachment factor B

L43631

19p13.3–p13.2

25.4 ± 2.6

10.3 ± 0.7

67%

2.5 ± 0.3

9.9E–02

2.8E–05

1.9E–03

 

MAPT

Microtubule-associated protein tau

AH005895

17q21.1

26.3 ± 4.6

10.1 ± 0.8

56%

2.4 ± 0.6

9.5E–02

2.2E–03

 

TPM3

Tropomyosin 3

BC000771

 

149.2 ± 16.9

64.5 ± 5.5

67%

2.3 ± 0.3

7.7E–02

1.7E–04

2.9E–02

 

HSU34301

Nonmuscle myosin heavy chain IIB

U34301

17

17.0 ± 2.1

7.4 ± 0.9

56%

2.3 ± 0.3

1.0E–01

1.2E–04

1.7E–02

 

KNS2

Kinesin 2 60/70kDa

L04733

14q32.3

16.1 ± 2.2

6.5 ± 0.4

56%

2.5 ± 0.3

6.5E–02

1.6E–04

2.4E–02

 

TUBB2C

Tubulin, β 2C

AK026167

9q34

53.2 ± 4.8

23.9 ± 2.5

67%

2.2 ± 0.2

1.7E–01

3.9E–05

3.2E–03

 

TUBA3

Tubulin, α 3

X01703

12q12–12q14.3

37.7 ± 5.5

14.5 ± 1.8

67%

2.4 ± 0.5

3.2E–01

9.7E–04

 

TNNC1

Troponin C, slow

M37984

3p21.3–p14.3

11.2± 1.2

5.1 ± 0.1

56%

2.2 ± 0.2*

6.7E–02

1.7E–04

2.7E–02

 

MSN

Moesin

M69066

Xq11.2–q12

178.8 ± 27.9

72.8 ± 6.9

67%

2.2 ± 0.6

5.4E–02

4.1 E–03

 
   

Transcription

       

RELA

V-rel reticuloendotheliosis viral oncogene homolog A

L19067

11q13

39.8 ± 4.3

11.1 ± 1.1

100%

3.6 ± 0.4

4.1E–03

7.9E–07

4.8E–06

1.964

FOS

V-fos FBJ murine osteosarcoma viral oncogene homolog

V01512

14q24.3

51.4 ± 14.0

13.9 ± 3.4

67%

3.4 ± 1.1

2.8E–02

4.5E–03

 

NFE2

Nuclear factor (erythroid-derived 2)

S77763

12q13

32.3 ± 4.1

9.5 ± 1.4

78%

3.4 ± 0.4

3.5E–01

1.5E–05

6.1 E–04

 

IRF5

Interferon regulatory factor 5

U51127

7q32

29.0 ± 4.6

10.2 ± 1.0

78%

2.9 ± 0.5

8.4E–02

2.0E–04

3.6E–02

 

ZNFpT1

Zinc-finger protein

X65230

 

15.2 ± 2.2

5.3 ± 0.1

78%

2.9 ± 0.4

6.4E–02

5.9E–04

 

SF1

Splicing factor 1

L49380

11q13

46.4 ± 4.3

16.2 ± 0.6

78%

2.9 ± 0.3

3.7E–02

1.5E–05

6.4E–04

2.307

HCFC1

Host cell factor C1

L20010

Xq28

26.0 ± 2.9

8.9 ± 0.5

78%

2.9 ± 0.3

2.7E–02

2.5E–05

1.6E–03

 

SREBF1

Sterol regulatory element binding transcription factor 1

U00968

17p11.2

25.6 ± 2.1

8.9 ± 0.6

89%

2.9 ± 0.2

6.3E–02

1.6E–06

1.9E–05

2.019

POLR2A

Polymerase (RNA) II (DNA directed) polypeptide A

X74874

17p13.1

18.9 ± 2.7

6.8 ± 0.5

67%

2.8 ± 0.4

7.3E–02

7.7E–05

8.7E–03

 

MAZ

MYC-associated zinc finger protein

M94046

16p11.2

29.7 ± 3.1

10.7 ± 0.6

78%

2.8 ± 0.3

7.9E–03

3.1E–05

2.3E–03

 

TCFL1

Transcription factor-like 1

D43642

1q21

38.2 ± 5.3

14.3 ± 0.7

67%

2.7 ± 0.4

9.9E–02

4.7E–04

 

IRF3

Interferon regulatory factor 3

Z56281

19q13.3–q13.4

25.1 ± 1.7

9.5 ± 0.5

78%

2.6 ± 0.2

2.2E–02

9.3E–07

6.5E–06

2.303

BTG2

BTG family, member 2

U72649

1q32

40.3 ± 8.1

14.8 ± 1.1

67%

2.5 ± 0.7

8.1E–02

3.0E–03

 

VGLL4

Vestigial like 4

D50911

3p25.2

16.4 ± 2.1

6.5 ± 0.3

67%

2.5 ± 0.3

1.3E–01

3.1 E–04

 

RNPC2

RNA-binding region (RNP1. RRM) containing 2

L10910

20q11.23

16.1 ± 2.1

6.4 ± 0.6

67%

2.5 ± 0.3

2.4E–01

4.7E–04

 

NBL1

Neuroblastoma, suppression of tumorigenicity 1

D28124

1p36.13–p36.11

16.6 ± 1.9

6.8 ± 0.6

67%

2.4 ± 0.3

2.4E–01

1.2E–04

1.6E–02

 

NCOR2

Nuclear receptor co-repressor 2

U37146

12q24

26.6 ± 2.9

11.2 ± 0.8

67%

2.4 ± 0.3

4.2E–02

5.1E–05

5.0E–03

 

JUND

Jun D proto-oncogene

X56681

19p13.2

114.4 ± 9.6

47.5 ± 3.9

89%

2.4 ± 0.2

1.4E–02

3.0E–06

4.8E–05

 

TRIM28

Tripartite motif-containing 28

U95040

19q13.4

44.0 ± 5.2

17.3 ± 1.2

67%

2.3 ± 0.5

1.4E–02

2.2E–04

4.0E–02

 

POLR2E

Polymerase (RNA) II (DNA directed) polypeptide E

D38251

19p13.3

28.4 ± 3.5

11.2 ± 1.1

78%

2.3 ± 0.5

7.7E–02

6.5E–04

 

BCL6

B-cell CLL/lymphoma 6 (zinc finger protein 51)

U00115

3q27

12.0 ± 2.1

5.2 ± 0.2

56%

2.3 ± 0.4

5.3E–02

2.6E–03

 

PML

Promyelocytic leukemia

M79462

15q22

10.7 ± 1.3

4.7 ± 0.2

56%

2.3 ± 0.3*

1.5E–02

5.1 E–04

 

CEBPB

CCAAT/enhancer binding protein (C/EBP), β

X52560

20

80.6 ± 14.7

32.2 ± 2.9

67%

2.2 ± 0.7

3.7E–01

1.3E–02

 

SFRS11

Splicing factor, arginine/serine-rich 11

M74002

1p31

20.0 ± 2.3

8.4 ± 0.8

78%

2.2 ± 0.5

1.4E–01

3.4E–04

 

SRF

Serum response factor

J03161

6p21.1

18.6 ± 2.5

8.3 ± 0.6

56%

2.2 ± 0.3

1.7E–01

3.9E–04

 

YY1

YY1 transcription factor

M77698

14q

13.4 ± 1.5

6.3 ± 0.6

56%

2.1 ± 0.2

2.2E–01

2.8E–04

 

LYL1

Lymphoblastic leukemia derived sequence 1

M22638

19p13.2

14.2 ± 1.2

6.8 ± 0.3

56%

2.1 ± 0.2

4.2E–02

4.3E–05

3.7E–03

 

SUPT4H1

Suppressor of Ty 4 homolog 1

U43923

17q21–q23

20.1 ± 3.2

8.9 ± 0.8

56%

2.0 ± 0.5

2.1E–01

2.9E–03

 

TAF15

TAF15 RNA polymerase II

U51334

17q11.1–q11.2

23.9 ± 2.8

11.1 ± 1.0

67%

1.9 ± 0.4

3.9E–02

6.5E–04

 
   

Translation

       

EIF3S9

Eukaryotic translation initiation factor 3, subunit 9 eta

U78525

7p22.3

19.6 ± 2.2

9.0 ± 0.7

67%

2.2 ± 0.2

2.3E–02

2.6E–04

4.8E–02

 
   

Transport

       

TCIRG1

T-cell, immune regulator 1, ATPase, H + transporting, lysosomal V0 protein a isoform 3

U45285

11q13.4–q13.5

31.4 ± 3.3

6.7 ± 0.5

100%

4.7 ± 0.5

1.2E–01

1.6E–07

1.6E–07

2.728

TETRAN

Tetracycline transporter-like protein

L11669

4p16.3

26.8 ± 2.7

6.8 ± 0.5

100%

3.9 ± 0.4

1.2E–01

1.6E–06

1.8E–05

2.404

HD

Huntingtin (Huntington disease)

L12392

4p16.3

22.3 ± 2.7

6.5 ± 0.3

78%

3.5 ± 0.4

9.1E–02

4.9E–05

4.6E–03

2.082

ATP6AP1

Human mRNA for ORF, Xq terminal portion

D16469

Xq28

31.7 ± 4.2

9.0 ± 0.8

89%

3.5 ± 0.5

6.5E–02

8.8E–06

2.9E–04

 

GGA3

Golgi associated, γ adaptin ear containing, ARF binding protein 3

D63876

17q25.2

33.9 ± 3.3

10.1 ± 0.6

89%

3.4 ± 0.3

7.1E–02

2.3E–06

3.2E–05

2.236

ATP6V0C

ATPase, H + transporting, lysosomal, VO subunit c

M62762

16p13.3

69.7 ± 8.8

21.2 ± 1.9

89%

3.3 ± 0.4

9.8E–02

4.3E–05

3.7E–03

 

AP2M1

Adaptor-related protein complex 2, mu 1 subunit

D63475

3q28

42.6 ± 5.5

14.2 ± 1.3

67%

3.0 ± 0.4

4.1E–02

1.3E–04

1.8E–02

 

SLC2A3

Solute carrier family 2 (facilitated glucose transporter), member 3

M20681

12p13.3

26.0 ± 2.3

9.3 ± 1.0

89%

2.8 ± 0.2

1.3E–01

9.2E–06

3.3E–04

 

SLC9A1

Solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na + /H +, amiloride sensitive)

S68616

1p36.1–p35

19.0 ± 2.4

6.8 ± 0.2

67%

2.8 ± 0.4

4.2E–02

2.3E–04

4.2E–02

 

SLC11A1

Solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1

D50402

2q35

19.1 ± 3.0

6.8 ± 0.6

78%

2.8 ± 0.4

1.9E–01

4.7E–04

 

MLC1

Megalencephalic leukoencephalopathy with subcortical cysts 1

D25217

22q13.33

16.1 ± 2.6

5.8 ± 0.5

56%

2.8 ± 0.4*

2.2E–02

5.7E–04

 

SEC24C

FLJ44715 gene product

D38555

10q22.3

21.3 ± 2.9

8.0 ± 0.6

67%

2.7 ± 0.4

8.3E–02

3.3E–04

 

CLTA

Clathrin, light polypeptide (Lea)

M20471

9p13

73.6 ± 9.1

26.7 ± 1.9

89%

2.8 ± 0.3

4.6E–02

3.8E–05

3.2E–03

 

AP2B1

Adaptor-related protein complex 2, β 1 subunit

M34175

17q11.2–q12

28.2 ± 4.0

10.3 ± 1.2

67%

2.5 ± 0.5

1.7E–01

2.3E–04

4.2E–02

 

AP1B1

Adaptor-related protein complex 1, β 1 subunit

L13939

22q12.2

23.2 ± 3.0

9.5 ± 0.8

67%

2.4 ± 0.3

4.3E–02

6.1E–04

 

TXN2

Thioredoxin 2

U78678

22q13.1

18.9 ± 2.5

7.5 ± 0.5

67%

2.5 ± 0.3

3.8E–02

2.8E–04

 

CRIP1

Cysteine-rich protein 1 (intestinal)

U09770

7q11.23

35.3 ± 3.9

15.9 ± 1.1

56%

2.2 ± 0.2

9.2E–02

1.4E–04

2.0E–02

 

NAPA

N-ethylmaleimide-sensitive factor attachment protein, alpha

U39412

19q13.33

15.0 ± 2.0

6.4 ± 0.4

67%

2.1 ± 0.5

5.5E–02

3.2E–03

 
   

Ubiquitin

       

UBE1

Ubiquitin-activating enzyme E1

M58028

Xp11.23

46.4 ± 6.9

11.3 ± 1.0

89%

4.1 ± 0.6

8.6E–03

3.3E–05

2.5E–03

 

USP11

Ubiquitin specific protease 11

U44839

Xp11.23

60.2 ± 7.4

18.9 ± 1.1

78%

3.2 ± 0.4

1.2E–02

5.0E–05

4.9E–03

 

UBC

Ubiquitin

M26880

12q24.3

198.0 ± 14.3

66.3 ± 10.5

89%

3.0 ± 0.2

2.4E–01

7.8E–06

2.4E–04

 

UBE1L

Ubiquitin-activating enzyme El-like

L13852

3p21

54.8 ± 4.6

18.6 ± 1.3

89%

2.9 ± 0.2

4.7E–02

9.4E–07

7.5E–06

1.966

CUL7

Cullin 7

D38548

6p21.1

14.7 ± 2.0

5.8 ± 0.3

56%

2.5 ± 0.3

6.6E–02

2.2E–04

4.0E–02

 

RAD23A

RAD23 homolog A (S. cerevisiae)

D21235

19p13.2

15.6 ± 1.6

6.6 ± 0.3

78%

2.4 ± 0.2

8.8E–02

2.0E–04

3.4E–02

 

UBE2V1

Homo sapiens UEV-1

BC000468

20q13.2

25.9 ± 3.6

11.2 ± 1.3

67%

2.3 ± 0.3

5.3E–01

4.4E–04

 

UFD1L

Ubiquitin like protein

U64444

22q11.21

22.8 ± 2.7

10.1 ± 0.9

67%

2.0 ± 0.4

1.3E–01

5.7E–04

 

USP4

Ubiquitin specific protease 4 (proto-oncogene)

U20657

3p21.3

14.8 ± 1.7

6.6 ± 0.3

67%

2.0 ± 0.4

4.0E–02

5.7E–04

  
   

Unknown

       

LRRC14

Leucine rich repeat containing 14

D25216

8q24.3

31.7 ± 4.1

9.2 ± 1.1

89%

3.4 ± 0.4

5.3E–02

8.8E–06

2.8E–04

 

WDR42A

WD repeat domain 42A

U06631

1q22–q23

23.6 ± 2.2

7.4 ± 0.5

89%

3.2 ± 0.3

8.1E–02

3.1E–06

5.6E–05

2.1

Clorf16

Chromosome 1 open reading frame 16

D87437

1q35

19.3 ± 2.2

6.5 ± 0.3

78%

3.0 ± 0.3

4.8E–02

2.8E–05

2.0E–03

2.116

Clorf19

Chromosome 6 open reading frame 9

U89336

6p21.3

41.6 ± 4.1

13.8 ± 1.3

78%

2.8 ± 0.3

7.6E–05

3.9E–06

8.1E–05

 

KIAA0056

KIAA0056 protein

D29954

11q25

17.4 ± 2.8

6.2 ± 0.4

67%

2.6 ± 0.6

2.7E–01

1.5E–03

 

C21orf2

Chromosome 21 open reading frame 2

U84569

21q22.3

25.2 ± 3.3

9.8 ± 0.9

67%

2.6 ± 0.3

8.5E–02

1.0E–04

1.2E–02

 

PRCC

Papillary renal cell carcinoma

X99720

1q21.1

20.1 ± 2.1

7.7 ± 0.6

78%

2.6 ± 0.3

1.4E–01

2.7E–05

1.8E–03

 

KIAA0226

KIAA0226 gene product

D86979

3q29

20.6 ± 2.3

7.8 ± 0.5

78%

2.6 ± 0.3

6.4E–02

5.4E–05

5.5E–03

 

ARMCX6

Hypothetical protein FLJ20811

L20773

Xq21.33–q22.3

25.6 ± 2.7

10.1 ± 0.9

56%

2.5 ± 0.3

4.6E–02

3.0E–05

2.1E–03

 

UBAP2L

Ubiquitin associated protein 2-like

D63478

1q22

13.2 ± 1.9

5.4 ± 0.2

67%

2.5 ± 0.3

5.5E–02

7.3E–04

 

ARMET

Arginine-rich, mutated in early stage tumors

M83751

3p21.1

21.2 ± 2.5

8.8 ± 0.5

56%

2.4 ± 0.3

4.9E–02

1.1E–04

1.5E–02

 

KIAA0174

KIAA0174 gene product

D79996

16q22.2

28.6 ± 3.2

12.0 ± 1.3

67%

2.4 ± 0.3

2.1E–01

1.1E–04

1.4E–02

 

TATDN2

TatD DNase domain containing 2

D86972

3p25.3

13.8 ± 1.5

5.8 ±0.5

67%

2.4 ±0.3

1.4E–01

1.0E–04

1.3E–02

 

PFAAP5

Phosphonoformate immuno-associated protein 5

U50535

13

15.7 ± 1.5

6.8 ±0.6

67%

2.3 ±0.2

1.7E–01

7.2E–05

8.0E–03

 

HSHRTPSN

Retrotransposon

Z48633

 

10.6 ± 2.1

4.4 ±0.2

44%

2.2 ±0.6*

7.9E–02

6.6E–03

 

TAGLN2

Transgelin 2

D21261

1q21–q25

278.8 ±30.1

111.3± 10.9

89%

2.2 ±0.5

1.6E–02

1.3E–03

 

TRIM26

Tripartite motif-containing 26

U09825

6p21.3

21.4 ± 2.8

9.6 ±0.6

56%

2.2 ±0.3

1.4E–01

1.0E–03

 

NUP 188

Nucleoporin 188kDa

D79991

9q34.13

13.7 ± 1.3

6.2 ±0.2

67%

2.2 ±0.2

4.2E–02

1.6E–04

2.3E–02

 

FAM53B

Family with sequence similarity 53, member B

D50930

10q26.2

16.8 ± 2.8

7.2 ±0.4

56%

2.1 ±0.5

9.7E–02

3.8E–03

 

C21orf33

Chromosome 21 open reading frame 33

U53003

21q22.3

12.2 ± 1.1

5.7 ±0.2

44%

2.1 ±0.2

6.7E–02

2.1E–05

1.2E–03

 

CYFIP2

Cytoplasmic FMR1 interacting protein 2

L47738

5q34

29.2 ±3.9

13.4 ± 1.2

67%

2.0 ±0.5

2.6E–02

1.4E–03

 

DXYS155E

DNA segment on chromosome X and Y (unique) 155 expressed sequence

L03426

Xp22.32, Ypter-p11.2

15.9 ± 2.1

6.7 ±0.4

78%

2.0 ± 0.5

2.5E–03

1.3E–03

 

BRD3

Bromodomain containing 3

D26362

9q34

15.9 ± 1.8

7.2 ±0.6

67%

2.0 ±0.4

2.6E–01

5.1E–04

 

FAM50A

DNA segment on chromosome X (unique) 9928 expressed sequence

D83260

Xq28

16.6 ± 1.7

7.6 ±0.4

33%

2.0 ± 0.2

6.3E–04

3.0E–05

2.2E–03

 

NK4

Natural killer cell transcript 4

M59807

16p13.3

116.7 ± 18.5

49.2 ±6.4

56%

1.9 ±0.6

6.7E–03

2.8E–03

 

Data are mean ± SE except aaverage ± SE. Genes were filtered based on the average frequency of 10 and average change in expression of at least 2-fold. Fold changes for genes with increased expression are represented as the ratio of RA average frequency/normal average frequency, whereas genes with reduced expression are represented as the negative reciprocal of that ratio. SE was also calculated for the fold change. Average frequency of expression and its SE were calculated for 9 RA and 13 control samples. The results of three separate statistical analyses performed on the data are shown. A Student t test was performed to identify statistically significant differences between samples with a threshold of P< 0.5. Two Welch ANOVA (26) analyses using different multiple testing corrections were performed. The first, performed according to the methods of Benjamini and Hochberg (28) to calculate the FDR, was used with a limit of 0.05. The second, based on Bonferroni (29,30) FWER, was calculated with P value cutoff of <0.05. The rightmost column represents genes that comprise the class prediction analysis. Chromosomal map units shown are based on GenBank information. *Genes with an asterisk have control samples with frequencies <5 ppm and are called absent in >50% of samples. Therefore, the fold change calculation may not accurately reflect the actual difference in expression. Annotation was based on GO, Gene, and PubMed to categorize the genes. Genes with different Affymetrix identifiers were not removed from the table.

Unsupervised Clustering

An unsupervised clustering analysis was performed on the 330 genes that passed the initial filtration, based on a hierarchical correlation coefficient algorithm (21). Samples were grouped based on similarity of expression. The resulting dendrogram describes the sample relationships by grouping the RA samples and controls by their expression patterns (Figure 1). Figure 1A depicts a region where expression levels in the RA samples were increased compared with the normal samples. This analysis suggests that there are significant differences in the gene expression of RA and control samples.
Figure 1

Unsupervised hierarchical cluster analysis of RNA from 9 RA and 13 control PBMC samples. Total RNA samples were analyzed on oligonucleotide arrays as described. In no case were samples pooled. Genes were selected for analysis if they had a present call, a frequency greater than 10 ppm, and two-fold change expression in five of nine RA samples. The expression patterns of 330 genes are displayed in a dendrogram where columns represent each sample and rows represent individual genes. Genes are colored on a gradient (from −10-fold to 10-fold), with those increase in expression relative to the average of the control in red. Those that decrease are in blue, and those with little or no change are in yellow. A, region where expression levels in the RA samples were increased compared with the normal samples.

ANOVA Analysis

To minimize the inclusion of genes not related to the disease state, several statistical approaches were used. The 330 transcripts that passed the initial filtration (Table 2) were subjected to a Student t test and a Welch ANOVA with two multiple testing corrections (22). To control for a proportion of genes that may appear in the analysis by chance, an FDR was calculated set to a threshold of 5%. This analysis defines a proportion of the genes that are expected to occur by chance relative to the total number of transcripts identified; 326 transcripts were called significant with this analysis (Table 2). In addition, the more stringent Bonferroni FWER using a P value cutoff of 0.05 was also performed, with 189 transcripts passing this analysis (Table 2).

Class Prediction

A k-nearest neighbor analysis was performed to identify a gene set that may distinguish the RA samples from normals. The prediction strength was evaluated using the 330 genes shown in Table 2. A list of predictor genes was assembled using the k-nearest neighbor method (26) to organize genes based on normalized expression levels. Cross-validation analyses comparing each sample to the model generated by the remaining samples were used to optimize the analysis parameters. This resulted in a number of neighbors value of 6 with a decision cutoff P value of 0.2 to predict expression patterns in RA vs. controls. Twenty-nine transcripts comprise the prediction gene set. The 29 prediction transcripts were grouped based on a hierarchical correlation to show the relationships (Figure 2).
Figure 2

Class prediction. Using a class prediction algorithm, a list of genes that most consistently distinguished diseased vs. normal samples was generated. Classification was generated by the k-nearest neighbors algorithm (26). The number of neighbors selected was six, with a decision cutoff for P value ratio of 0.2. The final list was determined by an iterative cross-validation process in which the best combination of number of genes and neighbors was found to derive the most discriminating list. In the cross-validation mode, each sample in turn was set aside as the test article, and the remainder of the samples were used to generate the model, which was then evaluated on the test article. (A) Fold change and P values of the 29 prediction genes. (B) Unsupervised hierarchical cluster analysis of the 29 genes. The expression patterns of 29 genes are displayed in a dendrogram where columns represent each sample and rows represent individual genes. Genes are colored on a gradient (from −10-fold to 10-fold) with those increase in expression relative to the average of the control in red. Those that decrease are in blue, and those with little or no change are in yellow.

Characterization of the RA Disease-Related Genes

The 330 differentially regulated transcripts were categorized into functional groups and are presented as the average fold change of RA frequency compared with that of the controls (Table 2). This analysis clustered the genes into 19 functional classes and highlighted one chromosomal location. Ten genes with increased expression in the RA PBMCs compared with normal controls map to an RA susceptibility locus, 6p21.3 (27) (Table 3). The functional classes are diverse and include genes involved in calcium binding, chaperones, cytokines, transcription, translation, signal transduction, extracellular matrix, integral to plasma membrane, integral to intracellular membrane, mitochondrial, ribosomal, structural, enzymes, and proteases. Many of these 330 genes or gene products are known to be differentially regulated in RA. Twenty-five genes were classified as unknown because they either coded for a hypothetical protein or were identified as an open reading frame of unknown function.
Table 3

Genes with increased expression in RA compared with normal PBMCs at the RA susceptibility locus 6p21.3

Gene symbol no.

Gene name

GenBank acc.

MLN

Motilin

X15393

AGPAT1

1-acylglycerol-3-phosphate O-acyltransferase 1

U56417

HLA-DQA1

Major histocompatibility complex, class II, DQ α 1

M34996

MICB

MHC class I chain-related gene B

U65416

HLA-DOA

Major histocompatibility complex, class II, DO alpha

M31525

BRD2

Bromodomain containing 2

X62083

STK19

Serine/threonine kinase 19

BC016916

RGL2

Ral guanine nucleotide dissociation stimulator-like 2

U68142

C1orf19

Chromosome 6 open reading frame 9

U89336

TRIM26

Tripartite motif-containing 26

U09825

The k-nearest neighbor analysis identified genes that may be preferentially regulated in the RA samples. Of the 29 genes identified by the class prediction analysis (Figure 2B) to be expressed in the RA PBMCs compared with the controls, only RELA (NFκB p65) (28), IGF2 (insulin-like growth factor 2) (29)], FTH1 (ferritin heavy chain) (30), and SELP (selectin P) (31) have previously been associated with RA. Furthermore, both NF-κB and selectin P have been used as therapeutic targets in animal models (32,33). INPP5E (inositol polyphosphate-5-phosphatase E), STAB1 (stabilin), AGPAT1 (1-acylglycerol-3-phosphate O-acyltransferase 1), TCIRG1 (T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A isoform 3), HD (Huntingtin), SREBF1 (sterol regulatory element binding factor 1), and IRF3 (interferon regulatory factor 3) are examples of genes that have not previously been associated with RA.

Discussion

In this study, the mRNA levels of 6800 genes were measured in PBMCs from RA patients with active disease and normal individuals. All patients were on DMARD therapy that included methotrexate. Three hundred thirty differentially expressed transcripts were detected in at least 50% of the patients and exhibited a minimum of a two-fold change in expression from normal individuals. A number of genes previously thought to be involved in RA pathogenesis were detected in this study. These include the transcripts for TNF receptor TNFRSF1B (p75) and CCL5 (RANTES). TNFa has a key role in RA, and the expression of mRNA and protein of TNF receptors is increased in RA synovial membranes and sera (34, 35, 36). In murine models, as well as TNFα transgenic and receptor knockout mice, the pathogenic activity of TNF has been well documented. Furthermore, both the soluble form of the TNF receptor and antibodies against TNF are efficacious in animal models and are effective therapies for RA (4,6–8,37,38). CCL5 is a chemokine expressed in the serum and synovial joints of patients with RA and is likely to play important roles in recruitment of inflammatory cells (39). A polyclonal antibody to RANTES improved symptoms in animals with adjuvant induced arthritis (40). RNA transcripts encoding proteins from a number of signaling pathways, including NF-κB, were present in increased amounts in individuals with RA, and many of these are targets for therapeutic blockade (41). NF-κB (RELA) has important roles in the production of inflammatory cytokines such as IL-1 and TNF (28). The presence of these known genes in the data set further validates the array data and analysis.

A k-nearest neighbor analysis was applied to the data set to identify genes preferentially expressed in the PBMCs from RA patients compared with controls. Twenty-nine genes were identified. Some of these genes have been previously identified as being differentially regulated in RA and include IGF2 (29), FTH1 (30), and SELP (31). SELP contributes to many inflammatory diseases and has been shown to mediate leukocyte interaction with endothelial cell wall (42). Levels of SELP are increased in the synovial fluid of RA patients (43). In the murine collagen-induced arthritis model, the deletion of SELP resulted in more severe disease compared with wild-type mice (44).

Many genes not previously known as being differently regulated in RA were also identified, for example, TCIRG1 (T-cell, immune regulator 1), INPP5E (inositol polyphosphate-5-phosphatase E), and STAB1 (stabilin). TCIRG1 is a seven-transmembrane, novel T cell protein that plays a role in T cell activation (45). Antibodies to TCIRG1 (TIRC7) prevent human T cell proliferation in vitro, inhibit type I subset-specific IFNγ and IL-2, but not the type II subset cytokine IL-4. A TIRC7 antibody prolonged survival in a rat model of acute kidney allograft rejection (45). TIRC7-null mice have disrupted T and B cell responses in vitro and in vivo, suggesting that TIRC7 may play a role in T and B lymphocyte balance (46).

INPP5E, a member of the inositol polyphosphate 5-phosphatase family, similar to INPP5D (Table 2), regulates PI-3 kinase signal transduction (47). AGPAT1 (1-acylglycerol-3-phosphate O-acyltransferase 1) catalyzes the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA). LPA and PA are two phospholipids involved in signal transduction and phospholipid synthesis (48). Overexpression of AGPAT-1 in cell lines leads to the expression of both TNF-α and IL-6 in cells stimulated with IL-1β, suggesting that AGPAT-1 overexpression may amplify cellular signaling responses from cytokines (49).

Interestingly, 10 transcripts, including AGPAT1, differentially regulated in the RA PBMC from this study map to chromosome region 6p21.3, the major histo-compatibility (MHC) locus III (27) (Table 3). Many of the genes in the MHCIII region have fundamental roles in a variety of cellular functions and include the inflammatory cytokines TNFα, LTA, LTB, and the advanced glycation end product receptor, RAGE (AGER) (27). Multifactor interactions contribute to the disease process at several levels. One hypothesis is that dysregulation of genes in a locus could contribute to the etiology of the disease, perhaps through coordinated transcription of regions of a chromosome in response to stress or inflammation. RA is a complex autoimmune disorder, and expression analysis of a larger number of patients may validate this hypothesis.

STAB1 [also known as common lymphatic endothelial and vascular receptor (CLEVER-1 or FEEL-1)] was overexpressed in the RA PBMCs. This gene, identified by the k-nearest neighbor analysis, was expressed in 100% of RA PBMC samples and exhibited the highest fold change in this study (64-fold). Stabilin 1 is a large glycoprotein, multifunction scavenger receptor. Characterized as FEEL-1, this protein demonstrated a role as a scavenger receptor that binds to both advanced glycation end products as well as gram-positive and gram-negative bacteria (50,51). The receptor was shown to be expressed on mononuclear cells, tissue macrophages, and endothelial cells (50, 51, 52). An antibody to FEEL-1 demonstrated a marked reduction in cell-to-cell interaction in a Matrigel tube formation assay, suggesting a role for the receptor in angiogenesis (50). CLEVER-1 has been demonstrated to be involved in the PMBC transmigration through vascular and lymphatic endothelium (52). The CLEVER-1 gene is encoded by 69 exons, and multiple isoforms are expressed in the endothelium (52). The potential function of CLEVER-1 in RA remains to be elucidated.

Several studies of gene expression in RA have been reported. Devauchelle et al. (53) focused on differences in expression in synovia isolated from RA patients compared with that of synovia from osteoarthritis patients. Watanabe et al. (54) reported on differences in expression between RA and normal synovial fibroblasts, and van der Pouw Kraan et al. (55) identified differences in gene expression in RA synovia, allowing the classification of different disease subtypes. A recent study by Bovin et al. (56), using a 12,000-gene oligonucleotide microarray, examined changes in gene expression between PBMCs from 14 RA patients vs. 7 sex-and age-matched controls, and they identified 25 genes that were discriminative. Although different filter criteria were applied to the data sets present here and the report from Bovin et al. (56), there were nine genes that overlapped between the two studies, including S100A12, NCF4, and GNG10. Of the genes that did not overlap, four were not present on the microarray used in this study, three showed changes but did not meet the strict data filtration criteria, and four were not called present in any of the samples. Another study by Olsen et al. (57), using a 4300-gene cDNA microarray, identified a gene expression signature for early-onset rheumatoid arthritis in PBMCs. In that study, the authors segregated the data based on those with longstanding and early-onset disease. There is some overlap between the Olsen et al. (57) study and the results presented here. Of the 44 genes identified, eight from Olsen, et al. also appeared in the present study. Of the 30 that do not, four were not on the human FL6800 array, 15 were not called present in any of the samples, and the others were not included due to the filtration criteria. In the results presented here, patients were selected from the high disease activity cohort, and during analysis, several filtration criteria were applied to the data set with several statistical analyses and a minimum expression criteria of at least 50% of the patients. These measures ensured that the resulting defined gene signature was as robust as possible.

It must be noted that RA patients possess a broad spectrum of disease severity and time of onset, and the comparisons above serve to highlight the multiple differences in patient selection criteria, study materials, protocols, and data analysis that exist in studies so far. Combining the data from our study with that of others, however, does point to several consistent changes in gene expression that would be useful to investigate further. For example, the increased expression of the RAGE ligand S100A12 has been observed in more than 1 study and, as a result, has highlighted the RAGE pathway as potentially important in RA; it is now subject to further study by our group.

The information from this study can be used in two major ways. First, it allows genes important in the pathogenesis of RA to be identified. These genes can then be investigated in detail to determine their potential roles in disease. Second, the power of DNA microarray profiling, with its ability to monitor the expression of multiple genes simultaneously, may allow the identification of patterns of gene expression associated with RA. This may enable rapid diagnosis of RA and predictions of prognosis, as well as response to, and side effects of, DMARDs. The use of these techniques is most advanced in oncology, where predictions of prognosis can be made for certain cancers (17). This provides clinically useful information that guides decisions about how aggressive a treatment regimen should be for a given patient. There is a marked difference in the clinical features of RA between individuals, and molecular phenotyping (or patient profiling) may identify or characterize different disease subgroups and courses of disease progression.

A weakness of global gene expression analysis techniques lies in identifying the relationship of changes in gene expression to the disease process. Changes in gene expression may either cause a disease process or occur as a consequence of it. The presence of gene expression changes in genes that have been associated with RA validates the data set. However, not all genes are primarily regulated by changes in mRNA levels, with many being subject to posttranscriptional regulation. TNF, the best-validated molecular therapeutic target in RA, does not emerge from this type of analysis. This study examined expression in nine RA patients and identified a set of genes that is preferentially expressed in RA patients compared with controls. Although the data are intriguing, samples from a larger number of patients would aid in a class prediction to determine which genes are most associated with disease state and type of prognosis. It is interesting to note that a recent study of PBMC expression profiles in several autoimmune diseases showed that, whereas all diseases displayed profiles that differed from a normal immune response, not all diseases could be clearly distinguished from each other (58).

Gene expression studies on PBMCs may not exactly represent the situation within the inflamed synovial membranes of RA. RA is a systemic disease, however, and differences in cytokine production and phenotype of PBMCs in RA have been demonstrated (59, 60, 61). This approach has the advantage of being a rapid and minimally invasive way of obtaining cells from patients. The usefulness of assaying tissue samples in RA is limited by availability and sampling bias due to regional differences in disease activity in synovia. However, if the diagnostic/predictive results of a gene expression profile can be demonstrated, PBMCs are a readily accessible source of cells.

The use of oligonucleotide microarrays enables a broader view of complex inflammatory diseases, such as RA. The simultaneous measurement of multiple mRNA transcripts allows an increased understanding of the complexity of proteins that may be interacting in a disease state rather than focusing on one or two at a time. This study identified 330 mRNA transcripts that were differentially regulated in the PBMCs from RA patients compared with normal volunteers. Having demonstrated that these techniques can be used with PBMCs, the next step involves looking at patterns of gene expression in individuals over time and detailed phenotypic examination of these individuals to determine patterns of gene expression associated with different features of RA.

Notes

Acknowledgments

The authors thank Dr. James C. Keith, Jr., for reviewing the manuscript.

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Copyright information

© Feinstein Institute for Medical Research 2007

Authors and Affiliations

  • Christopher J. Edwards
    • 1
    • 2
  • Jeffrey L. Feldman
    • 3
  • Jonathan Beech
    • 1
  • Kathleen M. Shields
    • 3
  • Jennifer A. Stover
    • 5
  • William L. Trepicchio
    • 4
  • Glenn Larsen
    • 6
  • Brian M. J. Foxwell
    • 1
  • Fionula M. Brennan
    • 1
  • Marc Feldmann
    • 1
  • Debra D. Pittman
    • 3
  1. 1.The Kennedy Institute of Rheumatology DivisionImperial College School of MedicineLondonUK
  2. 2.Department of RheumatologySouthampton General HospitalSouthamptonUK
  3. 3.Department of Cardiovascular and Metabolic DiseasesWyeth ResearchCambridgeUSA
  4. 4.Millennium PharmaceuticalsCambridgeUSA
  5. 5.AffymetrixSanta ClaraUSA
  6. 6.Hydra BiosciencesCambridgeUSA

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