Table 2 Functional grouping of genes differentially expressed between signature and non-signature IFNs

1)Metabolism/protein metabolism

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

ATP binding; DNA damage response, signal transduction resulting in cell cycle arrest; MAP kinase kinase kinase activity; activation of JUNK; activation of MAP/ERK kinase kinase; activation of MAPKK; cell cycle arrest; cell death; cell differentiation; cell proliferation; cellular_component unknown; protein amino acid phosphorylation; protein serine/threonine kinase activity; protein-tyrosine kinase activity; response to radiation; response to stress; transferase activity

Hs.115175

MMP9

matrix metalloproteinase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase)

collagen catabolism; collagenase activity; extracellular matrix; extracellular space; gelatinase B activity; hydrolase activity; zinc ion binding

Hs.151738

GAPD

glyceraldehyde-3-phosphate dehydrogenase

cytoplasm; glucose metabolism; glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity; glycolysis; oxidoreductase activity

Hs.169476

PRKRIR

protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)

DNA binding; negative regulation of cell proliferation; protein binding; regulation of translation; response to stress; signal transduction

Hs.177574

SRP14

signal recognition particle 14 kDa (homologous Alu RNA binding protein)

7S RNA binding; cotranslational membrane targeting; protein targeting; signal recognition particle

Hs.180394

MALT1

mucosa associated lymphoid tissue lymphoma translocation gene 1

activation of NF-kappaB-inducing kinase; anti-apoptosis; caspase activity; defense response; intracellular; peptidase activity; protein binding; proteolysis and peptidolysis; signal transduction

Hs.180566

PSMA7

proteasome (prosome, macropain) subunit, alpha type, 7

endopeptidase activity; proteasome core complex (sensu Eukarya); ubiquitin-dependent protein catabolism

Hs.233952

PSMA3 *

proteasome (prosome, macropain) subunit, alpha type, 7

endopeptidase activity; proteasome core complex (sensu Eukarya); ubiquitin-dependent protein catabolism

Hs.346918

LYZ

lysozyme (renal amyloidosis)

carbohydrate metabolism; cell wall catabolism; cytolysis; defense response to bacteria; extracellular space; hydrolase activity, acting on glycosyl bonds; inflammatory response; lysozyme activity

Hs.234734

MAFG

v-maf musculoaponeurotic fibrosarcoma oncogene homolog G (avian)

chromatin; nucleus; regulation of transcription, DNA-dependent; transcription factor activity; transcription from Pol II promoter

Hs.252229

NRBP

nuclear receptor binding protein

ATP binding; SH3/SH2 adaptor protein activity; nucleus; protein amino acid phosphorylation; protein kinase activity; receptor activity; signal transduction; transferase activity

Hs.272736

SCAND1

SCAN domain containing 1

RNA binding; nucleus; protein self binding; regulation of cell cycle; regulation of cell proliferation; regulation of transcription, DNA-dependent; transcription factor activity; transcription factor binding

Hs.274411

EEF1D

eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)

eukaryotic translation elongation factor 1 complex; guanyl-nucleotide exchange factor activity; protein biosynthesis; translation elongation factor activity; translational elongation

Hs.334798

NQO1

NAD(P)H dehydrogenase, quinone 1

NAD(P)H dehydrogenase (quinone) activity; cytochrome-b5 reductase activity; cytoplasm; electron transport; nitric oxide biosynthesis; oxidoreductase activity; response to toxin; synaptic transmission, cholinergic; xenobiotic metabolism

Hs.406515

FABP5

fatty acid binding protein 5 (psoriasis-associated)

cytoplasm; epidermal differentiation; fatty acid binding; lipid metabolism; transport; transporter activity

Hs.408061

S100A11

S100 calcium binding protein A11 (calgizzarin)

calcium ion binding; cytoplasm; negative regulation of DNA replication; negative regulation of cell proliferation; nucleus

Hs.417004

DIS155E

NRAS-related gene

DNA binding; RNA binding; male gonad development; regulation of transcription, DNA-dependent

Hs.69855

TAL1

T-cell acute lymphocytic leukemia 1

DNA binding; cell differentiation; cell proliferation; regulation of transcription, DNA-dependent

Hs.73828

PTPRN2

protein tyrosine phosphatase, receptor type, N polypeptide 2

hydrolase activity; integral to plasma membrane; protein amino acid dephosphorylation; protein-tyrosine-phosphatase activity; receptor activity; transmembrane receptor protein tyrosine phosphatase activity

Hs.74624

FKBP4

FK506 binding protein 4, 59 kDa

FK506 binding; Hsp70/Hsp90 organizing protein activity; biological_process unknown; cytoplasm; isomerase activity; nucleus; peptidyl-prolyl cis-trans isomerase activity; protein folding

Hs.848

LIPA

lipase A, lysosomal acid, cholesterol esterase (Wolman disease)

N-linked glycosylation; hydrolase activity; lipid catabolism; lipoprotein lipase activity; lysosome; sterol esterase activity

Hs.85226

ATF5

activating transcription factor 5

DNA binding; RNA polymerase II transcription factor activity; nucleus; regulation of cell cycle; regulation of transcription from Pol II promoter; transcription corepressor activity

Hs.9754

CD63*

lysosomal membrane glycoprotein

CD63 serves as an adaptor protein that links its interaction partners to the endocytic machinery of the cell/trafficking role

Hs.445570

LAMR1

laminin receptor 1 (ribosomal protein SA, 67 kDa)

cell adhesion; cell surface receptor linked signal transduction; cytosolic small ribosomal subunit (sensu Eukarya); integrin complex; intracellular; laminin receptor activity; protein biosynthesis; regulation of translation; structural constituent of ribosome

Hs.181357

2) Catalytic activity/hydrolase activity

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

51776

MMP9

matrix metalloproteinase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase)

(See description above)

Hs.151738

GAPD

glyceraldehyde-3-phosphate dehydrogenase

(See description above)

Hs.169476

MALT1

mucosa associated lymphoid tissue lymphoma translocation gene 1

(See description above)

Hs.180566

PSMA7

proteasome (prosome, macropain) subunit, alpha type, 7

(See description above)

Hs.233952

PSMA3 *

proteasome (prosome, macropain) subunit, alpha type, 7

(See description above)

Hs.346918

LYZ

lysozyme (renal amyloidosis)

(See description above)

Hs.234734

NRBP

nuclear receptor binding protein

(See description above)

Hs.272736

FLJ12671

hypothetical protein FLJ12671

exonuclease activity; hydrolase activity; nucleus

Hs.301904

NQO1

NAD(P)H dehydrogenase, quinone 1

(See description above)

Hs.406515

PTPRN2

protein tyrosine phosphatase, receptor type, N polypeptide 2

(See description above)

Hs.74624

FKBP4

FK506 binding protein 4, 59 kDa

(See description above)

Hs.848

LIPA

lipase A, lysosomal acid, cholesterol esterase (Wolman disease)

(See description above)

Hs.85226

3) Cell proliferation

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

PRKRIR

protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)

(See description above)

Hs.177574

SCAND1

SCAN domain containing 1

(See description above)

Hs.274411

H41

hypothetical protein H41

cell proliferation; cellular_component unknown; molecular_function unknown

Hs.283690

S100A11

S100 calcium binding protein A11 (calgizzarin)

(See description above)

Hs.417004

CD164

CD164 antigen, sialomucin

cell adhesion; development; endosome; hemopoiesis; immune response; integral to plasma membrane; membrane fraction; negative regulation of cell adhesion; negative regulation of cell proliferation; signal transduction; soluble fraction

Hs.43910

TAL1

T-cell acute lymphocytic leukemia 1

(See description above)

Hs.73828

ATF5

activating transcription factor 5

(See description above)

Hs.9754

IL-6

Interleukin 6

reactants also involved in the regulation of immune response, hematopoiesis, platelet production, acute phase reaction and bone resorption (susceptibility factor for osteopenia), playing a role in the aggressiveness of non hodgkin lymphoma by stimulating MMP2 and MMP9

Hs.512234

4) Cell growth and maintanance

SCA7

spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)

molecular_function unknown; nuclear organization and biogenesis; nucleus; visual perception

Hs.108447

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

TIP47

mannose-6-phosphate receptor binding protein 1

Golgi apparatus; endosome; receptor activity; vesicle-mediated transport

Hs.140452

PRKRIR

protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)

(See description above)

Hs.177574

SRP14

signal recognition particle 14 kDa (homologous Alu RNA binding protein)

(See description above)

Hs.180394

TUBB5

tubulin beta MGC4083

GTP binding; microtubule; microtubule-based movement; structural molecule activity

Hs.274398

SCAND1

SCAN domain containing 1

(See description above)

Hs.274411

H41

hypothetical protein H41

(See description above)

Hs.283690

FABP5

fatty acid binding protein 5 (psoriasis-associated)

(See description above)

Hs.408061

S100A11

S100 calcium binding protein A11 (calgizzarin)

(See description above)

Hs.417004

CD164

CD164 antigen, sialomucin

(See description above)

Hs.43910

CCL1

chemokine (C-C motif) ligand 1

calcium ion homeostasis; cell-cell signaling; chemokine activity; chemotaxis; extracellular space; immune response; inflammatory response; signal transduction; viral life cycle

Hs.72918

TAL1

T-cell acute lymphocytic leukemia 1

(See description above)

Hs.73828

ATF5

activating transcription factor 5

(See description above)

Hs.9754

5) Cell cycle

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

SCAND1

SCAN domain containing 1

(See description above)

Hs.274411

S100A11

S100 calcium binding protein A11 (calgizzarin)

(See description above)

Hs.417004

ATF5

activating transcription factor 5

(See description above)

Hs.9754

6) Regulation of transcription

MAFG

v-maf musculoaponeurotic fibrosarcoma oncogene homolog G (avian)

chromatin; nucleus; regulation of transcription, DNA-dependent; transcription factor activity; transcription from Pol II promoter

Hs.252229

SCAND1

SCAN domain containing 1

(See description above)

Hs.274411

D1S155E

NRAS-related gene

(See description above)

Hs.69855

TAL1

T-cell acute lymphocytic leukemia 1

(See description above)

Hs.73828

ATF5

activating transcription factor 5

(See description above)

Hs.9754

7) Nucleotide binding

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

KIFC3

kinesin family member C3

ATP binding; microtubule associated complex; motor activity

Hs.23131

NRBP

nuclear receptor binding protein

(See description above)

Hs.272736

TUBB-5

tubulin beta MGC4083

(See description above)

Hs.274398

8)Nucleobase nucleoside and nucleic acid metabolism

MAFG

v-maf musculoaponeurotic fibrosarcoma oncogene homolog G (avian)

(See description above)

Hs.252229

SCAND1

SCAN domain containing 1

(See description above)

Hs.274411

S100A11

S100 calcium binding protein A11 (calgizzarin)

(See description above)

Hs.417004

D1S155E

NRAS-related gene

(See description above)

Hs.69855

TAL-1

T-cell acute lymphocytic leukemia 1

(See description above)

Hs.73828

ATF-5

activating transcription factor 5

(See description above)

Hs.9754

9) Signal transducer activity

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

TIP47

mannose-6-phosphate receptor binding protein 1

Golgi apparatus; endosome; receptor activity; vesicle-mediated transport

Hs.140452

NRBP

nuclear receptor binding protein

(See description above)

Hs.272736

CCR1

chemokine (C-C motif) receptor 1

C-C chemokine receptor activity; G-protein signaling, coupled to cyclic nucleotide second messenger; cell adhesion; cell-cell signaling; chemotaxis; cytosolic calcium ion concentration elevation; immune response; inflammatory response; integral to plasma membrane; rhodopsin-like receptor activity

Hs.301921

CCL1

chemokine (C-C motif) ligand 1

calcium ion homeostasis; cell-cell signaling; chemokine activity; chemotaxis; extracellular space; immune response; inflammatory response; signal transduction; viral life cycle

Hs.72918

PTPRN2

protein tyrosine phosphatase, receptor type, N polypeptide 2

hydrolase activity; integral to plasma membrane; protein amino acid dephosphorylation; protein-tyrosine-phosphatase activity; receptor activity; transmembrane receptor protein tyrosine phosphatase activity

Hs.74624

10) Immune response/ defence

CD2BP2

CD2 antigen (cytoplasmic tail) binding protein 2

antimicrobial humoral response (sensu Vertebrata); cytoplasm

Hs.202677

LYZ

lysozyme (renal amyloidosis)

(See description above)

Hs.234734

CCR1

chemokine (C-C motif) receptor 1

(See description above)

Hs.301921

CD164

CD164 antigen, sialomucin

(See description above)

Hs.43910

CCL1

chemokine (C-C motif) ligand 1

(See description above)

Hs.72918

MALT1

mucosa associated lymphoid tissue lymphoma translocation gene 1

activation of NF-kappaB-inducing kinase; anti-apoptosis; caspase activity; defense response; intracellular; peptidase activity; protein binding; proteolysis and peptidolysis; signal transduction

Hs.180566

NKG7*

Natural killer cell group 7 sequence

Expressed in activated T cells, alpha LAK cells in kidney, liver, lung and pancreas. Not expressed in brain, heart, or skeletal muscle. Expressed at high levels in TCR gamma delta-expressing CTL clones, and in some TCR alpha beta-expressing CTL clones (both CD4+ and CD8+), but is not expressed in other TCR alpha beta-expressing CTL clones and in cell lines representing Bcells, monocytes, and myeloid cells

Hs.10306

NKTR*

NK cell tumor recognition protein

Activation of NK cell eleveted levels upon recognition of tumors by NK

Hs.432885

MPEG1*

likely ortholog of mouse macrophage expressed gene 1

Mpg-1 is a novel gene that may share a distant ancestry to perforin, a lytic protein found in cytotoxic T lymphocytes and natural killer cells

Hs.549280

CCL3L1*

chemokine (C-C motif) ligand 3-like 1

chemokine activity; chemotaxis; extracellular; immune response; inflammatory response; negative regulation of cell proliferation

Hs.387650

IL-6

Interleukin 6

(See description above)

Hs.512234

11) Cell adhesion

CCR1

chemokine (C-C motif) receptor 1

(See description above)

Hs.301921

CD164

CD164 antigen, sialomucin

(See description above)

Hs.43910

FKBP4

uncharacterized hematopoietic stem/progenitor cells protein MDS028

cell-matrix adhesion; integrin complex

Hs.848

LAMR1*

laminin receptor 1 (ribosomal protein SA, 67 kDa)

(See description above)

Hs.181357

ICAM3*

intracellular adhesion molecule 3

cell-cell adhesion; integral to plasma membrane; integrin binding; protein binding

Hs.99995

12) Development

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

FABP5

fatty acid binding protein 5 (psoriasis-associated)

cytoplasm; epidermal differentiation; fatty acid binding; lipid metabolism; transport; transporter activity

Hs.408061

KRT5

keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)

epidermal differentiation; intermediate filament; structural constituent of cytoskeleton

Hs.433845

CD164

CD164 antigen, sialomucin

(See description above)

Hs.43910

D1F155E

NRAS-related gene

(See description above)

Hs.69855

TAL1

T-cell acute lymphocytic leukemia 1

(See description above)

Hs.73828

13) Biosynthesis regulation of translation

PRKRIR

protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)

(See description above)

Hs.177574

EEF1D

eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)

(See description above)

Hs.334798

NQO1

NAD(P)H dehydrogenase, quinone 1

(See description above)

Hs.406515

LIPA

lipase A, lysosomal acid, cholesterol esterase (Wolman disease)

N-linked glycosylation; hydrolase activity; lipid catabolism; lipoprotein lipase activity; lysosome; sterol esterase activity

Hs.85226

LAMR1

laminin receptor 1 (ribosomal protein SA, 67 kDa)

(See description above)

Hs.181357

EEF2*

eukaryotic translation elongation factor 2

translational elongation, GTP binding translation elongation factor activity, protein biosynthesis

Hs.75309

EIF5A*

eukaryotic translation initiation factor 5A

regulation of translational initiation, nucleic acid binding, translation initiation factor activity, cytoplasm, viral genome replication, protein biosynthesis, translational initiation

Hs.534314

14)Cytoskeleton

KFC3

kinesin family member C3

ATP binding; microtubule associated complex; motor activity

Hs.23131

TUBB-5

tubulin beta MGC4083

(See description above)

Hs.274398

KRT5

keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)

epidermal differentiation; intermediate filament; structural constituent of cytoskeleton

Hs.433845

15)Transport

TIP47

mannose-6-phosphate receptor binding protein 1

(See description above)

Hs.140452

SRP14

signal recognition particle 14 kDa (homologous Alu RNA binding protein)

(See description above)

Hs.180394

TUBB-5

tubulin beta MGC4083

(See description above)

Hs.274398

FABP5

fatty acid binding protein 5 (psoriasis-associated)

(See description above)

Hs.408061

16) Cell Death

ZAK

sterile alpha motif and leucine zipper containing kinase AZK

(See description above)

Hs.115175

MALT1

mucosa associated lymphoid tissue lymphoma translocation gene 1

(See description above)

Hs.180566

LYZ

lysozyme (renal amyloidosis)

(See description above)

Hs.234734