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Table 2 cDNAs identified as differentially regulated by microarray analysis. Clone ID1 is the accession number of the cDNA feature on the microarray, when more than one cDNA feature was the same sequence the accession number for the feature with the highest fold difference is given, the number in brackets indicates the number of features identical and used in analysis. Identity2 is the functional protein assigned to the cDNA feature, Accession3 number relates to the identify of the protein. *indicates cDNA features where protein function is determined from NCBI UniGene as described in the text. Mean is the mean fold difference between the stimulated and non stimulated control cells.

From: Directional responses following recombinant cytokine stimulation of rainbow trout (Oncorhynchus mykiss) RTS-11 macrophage cells as revealed by transcriptome profiling

Clone ID1

Identity2

Accession3

Gene Ontology Identifier

Mean

SEM

Up regulated by rIFN-γ

CA063565(2)

Interferon regulatory factor 1

AAM77843

GO:0003700: transcription factor activity

12.1

4.9

CA062585(2)

Tapasin

ABE27285

GO:0019882: antigen presentation

11.4

3.5

CA063956

Complement C1q

XP_544507.2

GO:0006955: immune response

11.4

2.7

CB505764

C1q-like adipose specific protein

AAM73701

GO:0006955: immune response

10.6

5.8

CA062838*(2)

Acyl-coenzyme A-binding protein

AJ632152

GO:0006810: transport

10.3

1.4

CA051393*

Interferon consensus sequence binding protein (IRF-8)

NP_990747.1

GO:0003700: transcription factor activity

10.0

4.7

CA062698*

Ssa.15825

 

N/A

9.6

5.0

CB506130

Proteasome subunit beta type 1-A 20S

O09061

GO:0006511: ubiquitin-dependent protein catabolism

9.2

6.2

CA062737(3)

Low molecular mass protein 7

P28063

GO:0006955: immune response

8.8

3.3

CA052500

TAP 1

Q9JJ59

GO:0019882: antigen presentation

8.7

1.4

CA056108(2)

C-type lectin 2-1

Q91ZW7

GO:0006955: immune response

8.5

3.8

CA055080

Core histone macroH2A2.2; H2A histone family

AAH76893

GO:0044237 : cellular metabolism

7.6

4.3

CB516220(2)

Inhibitor of nuclear factor kappa B alpha

Q9Z1E3

GO:0006955: immune response

7.3

3.9

CA057910*

Programmed cell death 1 ligand 1

XP_424811.1

GO:0008219 : cell death

6.8

1.5

CA051372(2)

Low molecular mass protein 2

Q60692

GO:0006955: immune response

6.5

2.5

CB511048

VHSV-induced C-lectin-like protein

AY572832

GO:0006955: immune response

6.1

3.0

CA063009*(2)

Ssa.6457

 

N/A

6.0

1.7

CA052717*

Fc receptor-like 4

XP_547521.2

N/A

5.7

2.0

CA050149

IMMUNE-RESPONSIVE PROTEIN 1

XP_542615

N/A

4.1

1.6

CA050971

Proteasome subunit alpha type 6

Q9QUM9

GO:0006511: ubiquitin-dependent protein catabolism

3.8

1.5

CA063863*

Similar to interferon regulatory factor 1

NP_002189.1

GO:0003700: transcription factor activity

3.6

0.4

CA052613

Ubiquitin conjugating enzyme

XP_517968

GO:0006511: ubiquitin-dependent protein catabolism

3.6

0.6

CB500108

Ribosomal protein L35

AAM34649

GO:0006412: protein biosynthesis

3.4

0.8

CA044026(2)

MHC class I

L07605

GO:0019882: antigen presentation

3.4

0.4

CA052774

Protein phosphatase 2

P62715

GO:0044237 : cellular metabolism

3.0

0.5

CB511680(2)

Lysozyme

P17897

GO:0006952: defense response

3.0

0.3

CA055186

MECL1

P70195

GO:0006511: ubiquitin-dependent protein catabolism

2.7

0.5

CB493732

Proteasome subunit beta type 7

NP_989728.1

GO:0006511: ubiquitin-dependent protein catabolism

2.7

0.7

CA044982

HES1

Q9D172

N/A

2.6

0.7

CB496534(3)

Ferritin

P09528

GO:0006955: immune response

2.3

0.1

CA057391(2)

Granulin

XP_537620.2

GO:0008283: cell proliferation

2.2

0.4

CA060176

Galectin like protein

O08573

GO:0006952: defense response

2.2

0.3

CA060021

Unknown

 

N/A

2.2

0.2

CA046740

Sequestosome 1; oxidative stress induced

NP_035148

GO:0007165: signal transduction

2.1

0.1

Down regulated by rIFN-γ

CA057408

Annexin A2

P07356

GO:0050819 : negative regulation of coagulation

3.0

0.9

CB492780(2)

Id2 protein

P41136

GO:0045449: regulation of transcription

2.9

0.4

CA040487*

Ssa.17039

 

N/A

2.4

0.2

CK990422*

Ssa.2967

 

N/A

2.3

0.4

CA769647*

Ssa.3973

 

N/A

2.3

0.2

CB509992

18S ribosomal RNA gene, partial sequence

AY856868

N/A

2.1

0.1

CB491705

similar to PREDICTED: similar to ORF2

XP_425603.1

N/A

2.1

0.4

CB489453

Hypothetical protein 2

XP_417016

N/A

1.9

0.1

Up regulated by rIL-1β

CA050149

IMMUNE-RESPONSIVE PROTEIN 1

XP_542615

N/A

27.7

10.4

CB511048

VHSV-induced C-lectin-like

AY572832

GO:0006955: immune response

23.2

10.8

CA061271

UNKNOWN

 

N/A

21.2

9.8

CK991068(3)

Hepcidin

AAO85553

GO:0006952: defense response

21.2

5.0

CA055080

Core histone macroH2A2.2; H2A histone family

AAH76893

GO:0044237: cellular metabolism

20.7

2.2

CA037550

60S ribosomal protein L30

P62889

GO:0006412: protein biosynthesis

19.0

8.5

CB496842(3)

C-type lectin

Q91ZW7

GO:0006955: immune response

18.4

4.1

CA054326

Tax1 binding protein 1

NP_006015.4

GO:0007165: signal transduction

15.9

10.5

CA063656

Cyclin L1

AY606031

N/A

14.2

10.4

CB511230

TAP2

AF002180

GO:0019882: antigen presentation

13.0

6.4

CK990725

RhoE

P61588

GO:0007165: signal transduction

12.5

5.6

CB504496(3)

Differentially regulated trout protein 1

AAG30030

GO:0006955: immune response

12.3

4.5

CA063738*

Nuclear factor of k light polypeptide gene enhancer (p49/p100)

NP_989744.

GO:0007165: signal transduction

12.2

2.9

CB498152*

Similar to MARCKS-like 1

NP_075385.1

GO:0005516: calmodulin binding

12.2

3.2

CK990269*

Connexin 31

NP_990262.1

GO:0007154: cell communication

12.1

2.4

CB516988*

PREDICTED: similar to heparan sulfate proteoglycan

XP_417362.1

GO:0006917: induction of apoptosis

12.1

4.4

CB512516*

Ssa.2559

 

N/A

12.1

9.0

CB516929*

Ssa.5205

 

N/A

12.0

4.7

CA060421(2)

CD83

AAP93912

GO:0006952: defense response

11.5

4.8

CB514313

Delta 1

Q61483

GO:0007154: cell communication

11.1

7.2

CA063097*

Ssa.6200

 

N/A

11.1

3.6

CB511158(2)

Precerebellin-like protein

AAF04305

GO:0006952: defense response

10.7

5.3

CA041210

MARCKS-like protein

P28667

GO:0005516: calmodulin binding

9.8

1.7

CA059788(3)

Inhibitor of nuclear factor kappa B alpha

AAH62524

GO:0006955: immune response

9.6

2.6

CA044647*

Ssa.3390

 

N/A

9.6

0.9

CA060755*(2)

Ssa.2872

 

N/A

9.4

2.3

CA051323*

Ssa.6734

 

N/A

9.3

5.0

CA053062(3)

5-aminolevulinic acid synthase

Q8VC19

GO:0009058: biosynthesis

8.3

2.6

CA061251

RAS-related C3 botulinum substrate 2

Q05144

GO:0006952: defense response

8.2

4.6

CB507662*

Ssa.383

 

N/A

8.1

0.4

CB501098*

Ssa.3941

 

N/A

7.9

4.4

CA058223

Guanylate binding protein 4

Q01514

GO:0006955: immune response

7.8

2.8

CB515854*

Similar to tumor necrosis factor, alpha-induced protein 2

NP_006282.2

GO:0006952: defense response

7.8

1.1

CA052773

Arginyl-tRNA synthetase

Q9D0I9

GO:0009058: biosynthesis

7.2

4.5

CA050427*(3)

Ssa9019

 

N/A

7.2

1.6

CB498855(2)

6-phosphofructo-2-kinase

P70265

GO:0044237: cellular metabolism

7.0

1.2

CA046850

DEAD (Asp-Glu-Ala-Asp) box polypeptide 5

P17844

GO:0016049: cell growth

6.8

3.7

CA056715(3)

Transcription factor JUN-B

P09450

GO:0045449: regulation of transcription

6.5

0.7

CA063635*

Ssa.5016

 

N/A

6.5

3.4

CB514104

Adipophilin (Adipose differentiation-related protein)

P43883

GO:0006810: transport

6.3

0.7

CA038364

Similar to ubiquinol-cytochrome c reductase complex

P00130

GO:0044237: cellular metabolism

6.2

1.6

CA054114*

Ssa.25362

 

N/A

6.2

1.6

CA770328

Tapasin

ABE27285

GO:0019882: antigen presentation

5.8

1.5

CA054633

ATP-binding cassette transporter 2

P21440

GO:0006810: transport

5.5

1.7

CB501435*

Omy.30821

 

N/A

5.4

0.6

CA055219(2)

CCAAT/enhancer binding protein beta,

AAH49401

GO:0045449: regulation of transcription

5.0

0.8

CA062875

Similar to IFN consensus sequence binding protein IRF-8

Q90871

GO:0045449: regulation of transcription

5.0

1.4

CB517430

Similar to epithelial stromal interaction 1

NP_150280.1

N/A

4.9

1.5

CA053490

Tumour necrosis factor receptor

CAD57165

GO:0007165: signal transduction

4.8

1.1

CK990939

Adipose differentiation-related protein

Q9MZE5

GO:0016020: membrane

4.7

0.5

CA051393(2)

Similar to interferon consensus sequence binding protein

NP_990747.1

GO:0045449: regulation of transcription

4.7

1.2

CB511966

Factor VIII

Q06194

GO:0006952: defense response

4.4

0.7

CA043801

Ssa.22345

 

N/A

4.4

1.2

CA062585

TAPBP protein...

Q8UUL4

GO:0019882: antigen presentation

4.4

0.9

CA053654*

Ssa.7103

 

N/A

4.3

0.9

CA060783

Similar to protein tyrosine phosphatase

NP_035336.1

GO:0006464: protein modification

4.2

1.1

CB515947

Ssa.13995

 

N/A

4.2

1.0

CB515614

Ssa.4774

 

N/A

4.1

1.2

CB497913

Omy.8396

 

N/A

3.9

0.4

CB498900

Ssa.14843

 

N/A

3.9

1.0

CA767815

sequestosome 1

NP_035148

GO:0007165: signal transduction

3.8

0.4

CA056501

Serine (or cysteine) proteinase inhibitor

Q07235

N/A

3.7

0.7

CA044867

Ssa.8481

 

N/A

3.7

1.0

CB494479

Transcription factor ETV6

P97360

GO:0045449: regulation of transcription

3.7

0.3

CA063565

Interferon regulatory factor 1

AAM77843

GO:0045449: regulation of transcription

3.6

0.7

CB496486(2)

Low molecular mass protein 7

P28063

GO:0006955: immune response

3.5

0.6

CB498525

Secretory granule proteoglycan core protein

XP_507828.1

N/A

3.5

0.7

CB515392

Stomatin

P54116

GO:0007165: signal transduction

3.5

0.2

CA052717

similar to Fc receptor-like 4

XP_547521.2

N/A

3.4

0.2

CA052500

TAP1A

Q9JJ59

GO:0019882: antigen presentation

3.4

0.2

CB494116

UNKNOWN

 

N/A

3.3

0.8

CB489126

Protein translation factor SUI1

Q9CXU9

GO:0006412: protein biosynthesis

3.2

0.3

CK990998(3)

similar to Protein translation factor SUI1 homolog

P48024

GO:0006412: protein biosynthesis

3.2

0.3

CA062698

Ssa.15825

 

N/A

3.2

0.4

CB499179

Leucine-rich-repeat protein

XM_039906

GO:0006952: defense response;

3.1

0.4

CK991328

Omy.3531

 

N/A

3.1

1.0

CA062450*

Similar to melanoma cell adhesion molecule

NP_075548.1

GO:0007155: cell adhesion

3.1

0.5

CA051372

Low molecular mass protein 2

Q60692

GO:0006955: immune response

3.0

0.9

CA057910*

Similar to programmed cell death 1 ligand 1

XP_424811.1

GO:0006955: immune response

3.0

0.4

CA056074

p60

AAH01874

GO:0007165: signal transduction

2.9

0.3

CB488180

ATP synthase

Q9DCX2

GO:0015986: ATP synthesis coupled proton transport

2.9

0.2

CA052868

NADPH oxidase cytosolic protein p40phox

AB192468

GO:0007165: signal transduction

2.9

0.3

CA043996*

Ssa.3435

 

N/A

2.8

0.3

CB503379*

Ssa.7962

 

N/A

2.8

0.2

CB511558

UNKNOWN

 

N/A

2.7

0.3

CA060176

Galectin like protein

O08573

GO:0006952: defense response

2.6

0.2

CB502697*

Transmembrane 4 superfamily member 3

NP_598210.1

N/A

2.6

0.3

CB498077(4)

Ferritin

P09528

GO:0006955: immune response

2.5

0.1

CA039745

Alpha-globin

CAA65955

GO:0006810: transport

2.5

0.2

CA062784

UNKNOWN

 

N/A

2.5

0.2

CB493123

Activating transcription factor 4,

Q6T3V3

GO:0045449: regulation of transcription

2.4

0.3

CB488782

Growth regulated nuclear 68 protein

Q61656

GO:0045449: regulation of transcription

2.3

0.1

Down regulated by IL-1β

CA056515

UNKNOWN

 

N/A

5.4

2.8

CA041370

PREDICTED: similar to MAFB protein

XP_417353.1

GO:0045449: regulation of transcription

4.7

1.7

CA062828(3)

Id2 protein

P41136

GO:0045449: regulation of transcription

4.0

0.4

CB514524

xCDC46

BAA09949

GO:0045449: regulation of transcription

3.3

0.4

CB517923

Transforming protein myc

P01108

GO:0045449: regulation of transcription

3.1

0.7

CB502538

UNKNOWN

 

N/A

2.6

0.7

CA052685

Ribonucleotide reductase protein r2 class I

P11157

GO:0044237 : cellular metabolism

2.4

0.2