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

From: Delayed polarization of mononuclear phagocyte transcriptional program by type I interferon isoforms

GENENAME GENE DEESCRIPTION LOCUSLINK CLASSIFICATIONS UNIQID LOCUSLINK
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 51776
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 4318
GAPD glyceraldehyde-3-phosphate dehydrogenase cytoplasm; glucose metabolism; glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity; glycolysis; oxidoreductase activity Hs.169476 2597
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 5612
SRP14 signal recognition particle 14 kDa (homologous Alu RNA binding protein) 7S RNA binding; cotranslational membrane targeting; protein targeting; signal recognition particle Hs.180394 6727
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 10892
PSMA7 proteasome (prosome, macropain) subunit, alpha type, 7 endopeptidase activity; proteasome core complex (sensu Eukarya); ubiquitin-dependent protein catabolism Hs.233952 5688
PSMA3 * proteasome (prosome, macropain) subunit, alpha type, 7 endopeptidase activity; proteasome core complex (sensu Eukarya); ubiquitin-dependent protein catabolism Hs.346918 5684
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 4069
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 4097
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 29959
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 51282
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 1936
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 1728
FABP5 fatty acid binding protein 5 (psoriasis-associated) cytoplasm; epidermal differentiation; fatty acid binding; lipid metabolism; transport; transporter activity Hs.408061 2171
S100A11 S100 calcium binding protein A11 (calgizzarin) calcium ion binding; cytoplasm; negative regulation of DNA replication; negative regulation of cell proliferation; nucleus Hs.417004 6282
DIS155E NRAS-related gene DNA binding; RNA binding; male gonad development; regulation of transcription, DNA-dependent Hs.69855 7812
TAL1 T-cell acute lymphocytic leukemia 1 DNA binding; cell differentiation; cell proliferation; regulation of transcription, DNA-dependent Hs.73828 6886
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 5799
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 2288
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 3988
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 22809
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 29186
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 3921
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 4318
GAPD glyceraldehyde-3-phosphate dehydrogenase (See description above) Hs.169476 2597
MALT1 mucosa associated lymphoid tissue lymphoma translocation gene 1 (See description above) Hs.180566 10892
PSMA7 proteasome (prosome, macropain) subunit, alpha type, 7 (See description above) Hs.233952 5688
PSMA3 * proteasome (prosome, macropain) subunit, alpha type, 7 (See description above) Hs.346918 5684
LYZ lysozyme (renal amyloidosis) (See description above) Hs.234734 4069
NRBP nuclear receptor binding protein (See description above) Hs.272736 29959
FLJ12671 hypothetical protein FLJ12671 exonuclease activity; hydrolase activity; nucleus Hs.301904 81875
NQO1 NAD(P)H dehydrogenase, quinone 1 (See description above) Hs.406515 1728
PTPRN2 protein tyrosine phosphatase, receptor type, N polypeptide 2 (See description above) Hs.74624 5799
FKBP4 FK506 binding protein 4, 59 kDa (See description above) Hs.848 2288
LIPA lipase A, lysosomal acid, cholesterol esterase (Wolman disease) (See description above) Hs.85226 3988
3) Cell proliferation
ZAK sterile alpha motif and leucine zipper containing kinase AZK (See description above) Hs.115175 51776
PRKRIR protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) (See description above) Hs.177574 5612
SCAND1 SCAN domain containing 1 (See description above) Hs.274411 51282
H41 hypothetical protein H41 cell proliferation; cellular_component unknown; molecular_function unknown Hs.283690 55573
S100A11 S100 calcium binding protein A11 (calgizzarin) (See description above) Hs.417004 6282
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 8763
TAL1 T-cell acute lymphocytic leukemia 1 (See description above) Hs.73828 6886
ATF5 activating transcription factor 5 (See description above) Hs.9754 22809
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 3569
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 6314
ZAK sterile alpha motif and leucine zipper containing kinase AZK (See description above) Hs.115175 51776
TIP47 mannose-6-phosphate receptor binding protein 1 Golgi apparatus; endosome; receptor activity; vesicle-mediated transport Hs.140452 10226
PRKRIR protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) (See description above) Hs.177574 5612
SRP14 signal recognition particle 14 kDa (homologous Alu RNA binding protein) (See description above) Hs.180394 6727
TUBB5 tubulin beta MGC4083 GTP binding; microtubule; microtubule-based movement; structural molecule activity Hs.274398 84617
SCAND1 SCAN domain containing 1 (See description above) Hs.274411 51282
H41 hypothetical protein H41 (See description above) Hs.283690 55573
FABP5 fatty acid binding protein 5 (psoriasis-associated) (See description above) Hs.408061 2171
S100A11 S100 calcium binding protein A11 (calgizzarin) (See description above) Hs.417004 6282
CD164 CD164 antigen, sialomucin (See description above) Hs.43910 8763
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 6346
TAL1 T-cell acute lymphocytic leukemia 1 (See description above) Hs.73828 6886
ATF5 activating transcription factor 5 (See description above) Hs.9754 22809
5) Cell cycle
ZAK sterile alpha motif and leucine zipper containing kinase AZK (See description above) Hs.115175 51776
SCAND1 SCAN domain containing 1 (See description above) Hs.274411 51282
S100A11 S100 calcium binding protein A11 (calgizzarin) (See description above) Hs.417004 6282
ATF5 activating transcription factor 5 (See description above) Hs.9754 22809
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 4097
SCAND1 SCAN domain containing 1 (See description above) Hs.274411 51282
D1S155E NRAS-related gene (See description above) Hs.69855 7812
TAL1 T-cell acute lymphocytic leukemia 1 (See description above) Hs.73828 6886
ATF5 activating transcription factor 5 (See description above) Hs.9754 22809
7) Nucleotide binding
ZAK sterile alpha motif and leucine zipper containing kinase AZK (See description above) Hs.115175 51776
KIFC3 kinesin family member C3 ATP binding; microtubule associated complex; motor activity Hs.23131 3801
NRBP nuclear receptor binding protein (See description above) Hs.272736 29959
TUBB-5 tubulin beta MGC4083 (See description above) Hs.274398 84617
8)Nucleobase nucleoside and nucleic acid metabolism
MAFG v-maf musculoaponeurotic fibrosarcoma oncogene homolog G (avian) (See description above) Hs.252229 4097
SCAND1 SCAN domain containing 1 (See description above) Hs.274411 51282
S100A11 S100 calcium binding protein A11 (calgizzarin) (See description above) Hs.417004 6282
D1S155E NRAS-related gene (See description above) Hs.69855 7812
TAL-1 T-cell acute lymphocytic leukemia 1 (See description above) Hs.73828 6886
ATF-5 activating transcription factor 5 (See description above) Hs.9754 22809
9) Signal transducer activity
ZAK sterile alpha motif and leucine zipper containing kinase AZK (See description above) Hs.115175 51776
TIP47 mannose-6-phosphate receptor binding protein 1 Golgi apparatus; endosome; receptor activity; vesicle-mediated transport Hs.140452 10226
NRBP nuclear receptor binding protein (See description above) Hs.272736 29959
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 1230
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 6346
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 5799
10) Immune response/ defence
CD2BP2 CD2 antigen (cytoplasmic tail) binding protein 2 antimicrobial humoral response (sensu Vertebrata); cytoplasm Hs.202677 10421
LYZ lysozyme (renal amyloidosis) (See description above) Hs.234734 4069
CCR1 chemokine (C-C motif) receptor 1 (See description above) Hs.301921 1230
CD164 CD164 antigen, sialomucin (See description above) Hs.43910 8763
CCL1 chemokine (C-C motif) ligand 1 (See description above) Hs.72918 6346
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 10892
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 4818
NKTR* NK cell tumor recognition protein Activation of NK cell eleveted levels upon recognition of tumors by NK Hs.432885 4820
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 219972
CCL3L1* chemokine (C-C motif) ligand 3-like 1 chemokine activity; chemotaxis; extracellular; immune response; inflammatory response; negative regulation of cell proliferation Hs.387650 6349
IL-6 Interleukin 6 (See description above) Hs.512234 3569
11) Cell adhesion
CCR1 chemokine (C-C motif) receptor 1 (See description above) Hs.301921 1230
CD164 CD164 antigen, sialomucin (See description above) Hs.43910 8763
FKBP4 uncharacterized hematopoietic stem/progenitor cells protein MDS028 cell-matrix adhesion; integrin complex Hs.848 55846
LAMR1* laminin receptor 1 (ribosomal protein SA, 67 kDa) (See description above) Hs.181357 3921
ICAM3* intracellular adhesion molecule 3 cell-cell adhesion; integral to plasma membrane; integrin binding; protein binding Hs.99995 3385
12) Development
ZAK sterile alpha motif and leucine zipper containing kinase AZK (See description above) Hs.115175 51776
FABP5 fatty acid binding protein 5 (psoriasis-associated) cytoplasm; epidermal differentiation; fatty acid binding; lipid metabolism; transport; transporter activity Hs.408061 2171
KRT5 keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types) epidermal differentiation; intermediate filament; structural constituent of cytoskeleton Hs.433845 3852
CD164 CD164 antigen, sialomucin (See description above) Hs.43910 8763
D1F155E NRAS-related gene (See description above) Hs.69855 7812
TAL1 T-cell acute lymphocytic leukemia 1 (See description above) Hs.73828 6886
13) Biosynthesis regulation of translation
PRKRIR protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) (See description above) Hs.177574 5612
EEF1D eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein) (See description above) Hs.334798 1936
NQO1 NAD(P)H dehydrogenase, quinone 1 (See description above) Hs.406515 1728
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 3988
LAMR1 laminin receptor 1 (ribosomal protein SA, 67 kDa) (See description above) Hs.181357 3921
EEF2* eukaryotic translation elongation factor 2 translational elongation, GTP binding translation elongation factor activity, protein biosynthesis Hs.75309 1938
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 1984
14)Cytoskeleton
KFC3 kinesin family member C3 ATP binding; microtubule associated complex; motor activity Hs.23131 3801
TUBB-5 tubulin beta MGC4083 (See description above) Hs.274398 84617
KRT5 keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types) epidermal differentiation; intermediate filament; structural constituent of cytoskeleton Hs.433845 3852
15)Transport
TIP47 mannose-6-phosphate receptor binding protein 1 (See description above) Hs.140452 10226
SRP14 signal recognition particle 14 kDa (homologous Alu RNA binding protein) (See description above) Hs.180394 6727
TUBB-5 tubulin beta MGC4083 (See description above) Hs.274398 84617
FABP5 fatty acid binding protein 5 (psoriasis-associated) (See description above) Hs.408061 2171
16) Cell Death
ZAK sterile alpha motif and leucine zipper containing kinase AZK (See description above) Hs.115175 51776
MALT1 mucosa associated lymphoid tissue lymphoma translocation gene 1 (See description above) Hs.180566 10892
LYZ lysozyme (renal amyloidosis) (See description above) Hs.234734 4069
  1. Genes in blue rectangles are up-regulated in MP stimulated by "signature IFNs" (and down-regulated in non-signature interferons). Genes in orange rectangles are up-regulated in MP stimulated by non-signature IFN (and downregulated in signature interferons). Genes belonging to more than one functional group may represent central and shared switches in pathways directly influenced by IFNs' activity. Genes in torqoise characters did not classify in any of the categories mined by DAVID software (PSMA3, NKTR, NKG7, CD63, EEF2) and were manually entered in the appropriate group on the basis of Entrez cross database annotation and Genecard http://www.ncbi.nlm.nih.gov/Entrez; http://bioinfo.weizmann.ac.il/cards/index.shtml