Table 1

Genes at least two-fold different between PCNSL and non-CNS DLBCL at P < 0.05

GenesFold ChangePDescription
CNS versus non-CNS up-regulated 
    SPP1 9.73 < .001 Secreted phosphoprotein 1 (osteopontin) 
    TF 8.33 < .001 Transferrin 
    DDR1 6.08 < .001 Discoidin domain receptor family, member 1 
    NM_178012 5.13 < .001 Tubulin, beta polypeptide paralog 
    SERPINA3 4.67 < .001 Serine (or cysteine) proteinase inhibitor, clade A, member 3 
    S-100B 4.07 < .001 S-100 calcium binding protein, beta (neural) 
    C9orf58 4.03 < .001 Chromosome 9 open reading frame 58 
    BC020630 3.61 < .001 Calcium/calmodulin-dependent protein kinase II 
    CRYAB 3.36 < .001 Crystallin, alpha B (CRYAB) 
    NM_018584 3.26 < .001 Calcium/calmodulin-dependent protein kinase II 
    AF034208 3.24 .015 RIG-like 7–1 mRNA, complete cds 
    CXCL13 3.22 .009 Chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant) 
    NM_152680 3.01 .032 Hypothetical protein FLJ32028 (FLJ32028) 
    TCL1A 2.96 < .001 T-cell leukemia/lymphoma 1A 
    DKK3 2.91 < .001 Dickkopf homolog 3 
    FOXG1B 2.85 .003 Forkhead box G1B 
    UGT2B17 2.81 .041 UDP glycosyltransferase 2 family, polypeptide B17 
    TACSTD1 2.79 .006 Tumor-associated calcium signal transducer 1 
    FEZ1 2.78 .004 Fasciculation and elongation protein zeta 1 (zygin I) 
    CHI3L1 2.72 < .001 Chitinase 3-like 1 (cartilage glycoprotein-39) 
    CA2 2.7 < .001 Carbonic anhydrase II 
    MGST1 2.64 .037 Microsomal glutathione S-transferase, transcript variant 1c 
    DNAJC12 2.63 < .001 DnaJ (Hsp40) homolog, subfamily C, member 12 
    AK097976 2.6 .026 cDNA FLJ40657 fis, clone THYMU2019436 
    NM_018357 2.57 .042 Acheron (FLJ11196) 
    HBA2 2.5 .019 Hemoglobin, alpha 2 (HBA2) 
    NM_024897 2.44 .01 Progestin and adipoQ receptor family member VI (PAQR6) 
    RGS13 2.4 .027 Regulator of G-protein signalling 13 
    FCGR3A 2.37 .004 Fc fragment of IgG, low affinity IIIa, receptor for (CD16) 
    CNP 2.25 < .001 2′,3′-cyclic nucleotide 3′ phosphodiesterase 
    FBP1 2.24 .04 Fructose-1,6-bisphosphatase 1 
    BC000525 2.21 .001 Glutamic-oxaloacetic transaminase 2 
    BMP7 2.11 .017 Bone morphogenetic protein 7 
    NM_013332 2.08 .021 Hypoxia-inducible protein 2 (HIG2) 
    C1QB 2.03 .023 Complement component 1, q subcomponent, beta polypeptide 
    IRF4 2.02 .004 Interferon regulatory factor 4 
    DECR2 2.01 .006 2,4-dienoyl CoA reductase 2 
CNS versus non-CNS down-regulated 
    CX3CR1 0.5 .003 Chemokine (C-X3-C motif) receptor 1 
    AK091178 0.49 .042 cDNA FLJ33859 fis, clone CTONG2006223 
    D42043 0.49 .002 KIAA0084 mRNA, partial cds 
    SQLE 0.49 .004 Squalene epoxidase (SQLE) 
    P2RY8 0.49 .006 Purinergic receptor P2Y, G-protein coupled, 8 
    LXN 0.48 .026 Latexin 
    LPP 0.47 .002 LIM domain containing preferred translocation partner in lipoma 
    S56205 0.47 .005 Insulin-like growth factor binding protein 3 {3′ region} 
    Z24727 0.47 .008 Tropomyosin isoform mRNA, complete CDS 
    STEAP 0.46 .015 Six transmembrane epithelial antigen of the prostate 
    COL6A1 0.45 < .001 Collagen, type VI, alpha 1 
    COL12A1 0.45 .002 Collagen, type XII, alpha 1 
    AK022110 0.44 .023 cDNA FLJ12048 fis, clone HEMBB1001990 
    NR2F2 0.43 .006 Nuclear receptor subfamily 2, group F, member 2 
    NNMT 0.43 < .001 Nicotinamide N-methyltransferase 
    AK091153 0.42 .006 cDNA FLJ33834 fis, clone CTONG2004264 
    BC040354 0.42 < .001 Caldesmon 1, transcript variant 3 
    VEGFC 0.4 .001 Vascular endothelial growth factor C 
    LAMA4 0.37 .008 Laminin, alpha 4 
    NM_015714 0.32 < .001 Putative lymphocyte G0/G1 switch gene (G0S2) 
    CAMKK2 0.3 .026 Calcium/calmodulin-dependent protein kinase kinase 2, beta 
    FBN1 0.29 .001 Fibrillin 1 (Marfan syndrome) 
    AJ001381 0.28 .002 Incomplete cDNA for a mutated allele of a myosin class I, myh-1c 
    LUM 0.28 .008 Lumican (LUM) 
    LOXL1 0.27 .001 Lysyl oxidase-like 1 
    COL1A2 0.27 < .001 Collagen, type I, alpha 2 
GenesFold ChangePDescription
CNS versus non-CNS up-regulated 
    SPP1 9.73 < .001 Secreted phosphoprotein 1 (osteopontin) 
    TF 8.33 < .001 Transferrin 
    DDR1 6.08 < .001 Discoidin domain receptor family, member 1 
    NM_178012 5.13 < .001 Tubulin, beta polypeptide paralog 
    SERPINA3 4.67 < .001 Serine (or cysteine) proteinase inhibitor, clade A, member 3 
    S-100B 4.07 < .001 S-100 calcium binding protein, beta (neural) 
    C9orf58 4.03 < .001 Chromosome 9 open reading frame 58 
    BC020630 3.61 < .001 Calcium/calmodulin-dependent protein kinase II 
    CRYAB 3.36 < .001 Crystallin, alpha B (CRYAB) 
    NM_018584 3.26 < .001 Calcium/calmodulin-dependent protein kinase II 
    AF034208 3.24 .015 RIG-like 7–1 mRNA, complete cds 
    CXCL13 3.22 .009 Chemokine (C-X-C motif) ligand 13 (B-cell chemoattractant) 
    NM_152680 3.01 .032 Hypothetical protein FLJ32028 (FLJ32028) 
    TCL1A 2.96 < .001 T-cell leukemia/lymphoma 1A 
    DKK3 2.91 < .001 Dickkopf homolog 3 
    FOXG1B 2.85 .003 Forkhead box G1B 
    UGT2B17 2.81 .041 UDP glycosyltransferase 2 family, polypeptide B17 
    TACSTD1 2.79 .006 Tumor-associated calcium signal transducer 1 
    FEZ1 2.78 .004 Fasciculation and elongation protein zeta 1 (zygin I) 
    CHI3L1 2.72 < .001 Chitinase 3-like 1 (cartilage glycoprotein-39) 
    CA2 2.7 < .001 Carbonic anhydrase II 
    MGST1 2.64 .037 Microsomal glutathione S-transferase, transcript variant 1c 
    DNAJC12 2.63 < .001 DnaJ (Hsp40) homolog, subfamily C, member 12 
    AK097976 2.6 .026 cDNA FLJ40657 fis, clone THYMU2019436 
    NM_018357 2.57 .042 Acheron (FLJ11196) 
    HBA2 2.5 .019 Hemoglobin, alpha 2 (HBA2) 
    NM_024897 2.44 .01 Progestin and adipoQ receptor family member VI (PAQR6) 
    RGS13 2.4 .027 Regulator of G-protein signalling 13 
    FCGR3A 2.37 .004 Fc fragment of IgG, low affinity IIIa, receptor for (CD16) 
    CNP 2.25 < .001 2′,3′-cyclic nucleotide 3′ phosphodiesterase 
    FBP1 2.24 .04 Fructose-1,6-bisphosphatase 1 
    BC000525 2.21 .001 Glutamic-oxaloacetic transaminase 2 
    BMP7 2.11 .017 Bone morphogenetic protein 7 
    NM_013332 2.08 .021 Hypoxia-inducible protein 2 (HIG2) 
    C1QB 2.03 .023 Complement component 1, q subcomponent, beta polypeptide 
    IRF4 2.02 .004 Interferon regulatory factor 4 
    DECR2 2.01 .006 2,4-dienoyl CoA reductase 2 
CNS versus non-CNS down-regulated 
    CX3CR1 0.5 .003 Chemokine (C-X3-C motif) receptor 1 
    AK091178 0.49 .042 cDNA FLJ33859 fis, clone CTONG2006223 
    D42043 0.49 .002 KIAA0084 mRNA, partial cds 
    SQLE 0.49 .004 Squalene epoxidase (SQLE) 
    P2RY8 0.49 .006 Purinergic receptor P2Y, G-protein coupled, 8 
    LXN 0.48 .026 Latexin 
    LPP 0.47 .002 LIM domain containing preferred translocation partner in lipoma 
    S56205 0.47 .005 Insulin-like growth factor binding protein 3 {3′ region} 
    Z24727 0.47 .008 Tropomyosin isoform mRNA, complete CDS 
    STEAP 0.46 .015 Six transmembrane epithelial antigen of the prostate 
    COL6A1 0.45 < .001 Collagen, type VI, alpha 1 
    COL12A1 0.45 .002 Collagen, type XII, alpha 1 
    AK022110 0.44 .023 cDNA FLJ12048 fis, clone HEMBB1001990 
    NR2F2 0.43 .006 Nuclear receptor subfamily 2, group F, member 2 
    NNMT 0.43 < .001 Nicotinamide N-methyltransferase 
    AK091153 0.42 .006 cDNA FLJ33834 fis, clone CTONG2004264 
    BC040354 0.42 < .001 Caldesmon 1, transcript variant 3 
    VEGFC 0.4 .001 Vascular endothelial growth factor C 
    LAMA4 0.37 .008 Laminin, alpha 4 
    NM_015714 0.32 < .001 Putative lymphocyte G0/G1 switch gene (G0S2) 
    CAMKK2 0.3 .026 Calcium/calmodulin-dependent protein kinase kinase 2, beta 
    FBN1 0.29 .001 Fibrillin 1 (Marfan syndrome) 
    AJ001381 0.28 .002 Incomplete cDNA for a mutated allele of a myosin class I, myh-1c 
    LUM 0.28 .008 Lumican (LUM) 
    LOXL1 0.27 .001 Lysyl oxidase-like 1 
    COL1A2 0.27 < .001 Collagen, type I, alpha 2 
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