Table 1.

The most significantly differentially expressed genes in CNS and nodal large B-cell lymphomas

Gene function and accession no.
Name
FDR
RAWP
CNS/LN ratio
Genes with higher level of expression in PCNSL     
   Cell cycle, proliferation, and growth      
      W87741   v-Myc myelocytomatosis viral oncogene homolog   0.0056   < .001   2.74  
      AA464689   Myc-induced nuclear antigen   0.0062   < .001   1.54  
      AA669443   Eukaryotic translation initiation factor 5   0.0043   < .001   2.02  
      H56918   Eukaryotic translation initiation factor 4A   0.0043   < .001   5.58  
      AA086475   Cullin 5   0.0077   < .001   2  
      AA455521   E2F5 transcription factor 5   0.0077   < .001   4.2  
      H38804   Mitotic checkpoint protein BUB 3   0.0089   .005   2.55  
      AA453663   Pim-1   0.035   .005   2.46  
      AA284634   Janus kinase 1   0.056   .009   1.86  
   Unfolded protein response      
      W90128   X-box binding protein 1   0.0043   < .001   4.59  
      AA707661   Activating transcription factor 6   0.001   < .001   1.87  
   Programmed cell death      
      W01536   Programmed cell death 4   0.0043   < .001   5.41  
      W70189   Fas (TNFRSF6)-associated factor 1   0.0043   < .001   2.22  
      N94588   Caspase-8 and FADD-like apoptosis regulator   0.064   .01   2.2  
   Invasion, adhesion, stromal environment      
      AA425451   Integrin alpha E (CD103)   0.036   .005   1.79  
      N20475   Cathepsin-D   0.0056   < .001   2.35  
Genes with lower level of expression in PCNSL     
   Transcription factor      
      AA001604   Zinc finger 36   0.0056   .002   0.56  
      AA701046   Myeloid/lymphoid or mixed lineage leukemia   0.0043   .001   0.49  
      H84982   Checkpoint suppressor 1   0.015   < .001   0.36  
   Signal transduction      
      AA455591   EphB3   0.0043   .001   0.56  
      H67666   Ribosomal S6 kinase, 90 kDa, polypeptide 3   0.0099   < .001   0.43  
      AA148524   Discoidin domain receptor family member 2   0.0043   < .001   0.47  
   Invasion, adhesion, stromal environment      
      AA099554   Disintegrin and metalloprotease domain 12   0.009   < .001   0.42  
      AA936799   Matrix metalloprotease 2   0.0056   < .001   0.15  
      AA430540   Collagen type IV alpha 2   0.01   < .001   0.5  
      R75636   Collagen type V alpha 1   0.015   .001   0.54  
      H16637   Vascular cell adhesion molecule 1   0.034   .005   0.49  
      H97778   E-cadherin   0.039   .006   0.48  
      N64384
 		 Integrin alpha X (CD11C)
 		 0.025
 		 .003
 		 0.32
 
Gene function and accession no.
Name
FDR
RAWP
CNS/LN ratio
Genes with higher level of expression in PCNSL     
   Cell cycle, proliferation, and growth      
      W87741   v-Myc myelocytomatosis viral oncogene homolog   0.0056   < .001   2.74  
      AA464689   Myc-induced nuclear antigen   0.0062   < .001   1.54  
      AA669443   Eukaryotic translation initiation factor 5   0.0043   < .001   2.02  
      H56918   Eukaryotic translation initiation factor 4A   0.0043   < .001   5.58  
      AA086475   Cullin 5   0.0077   < .001   2  
      AA455521   E2F5 transcription factor 5   0.0077   < .001   4.2  
      H38804   Mitotic checkpoint protein BUB 3   0.0089   .005   2.55  
      AA453663   Pim-1   0.035   .005   2.46  
      AA284634   Janus kinase 1   0.056   .009   1.86  
   Unfolded protein response      
      W90128   X-box binding protein 1   0.0043   < .001   4.59  
      AA707661   Activating transcription factor 6   0.001   < .001   1.87  
   Programmed cell death      
      W01536   Programmed cell death 4   0.0043   < .001   5.41  
      W70189   Fas (TNFRSF6)-associated factor 1   0.0043   < .001   2.22  
      N94588   Caspase-8 and FADD-like apoptosis regulator   0.064   .01   2.2  
   Invasion, adhesion, stromal environment      
      AA425451   Integrin alpha E (CD103)   0.036   .005   1.79  
      N20475   Cathepsin-D   0.0056   < .001   2.35  
Genes with lower level of expression in PCNSL     
   Transcription factor      
      AA001604   Zinc finger 36   0.0056   .002   0.56  
      AA701046   Myeloid/lymphoid or mixed lineage leukemia   0.0043   .001   0.49  
      H84982   Checkpoint suppressor 1   0.015   < .001   0.36  
   Signal transduction      
      AA455591   EphB3   0.0043   .001   0.56  
      H67666   Ribosomal S6 kinase, 90 kDa, polypeptide 3   0.0099   < .001   0.43  
      AA148524   Discoidin domain receptor family member 2   0.0043   < .001   0.47  
   Invasion, adhesion, stromal environment      
      AA099554   Disintegrin and metalloprotease domain 12   0.009   < .001   0.42  
      AA936799   Matrix metalloprotease 2   0.0056   < .001   0.15  
      AA430540   Collagen type IV alpha 2   0.01   < .001   0.5  
      R75636   Collagen type V alpha 1   0.015   .001   0.54  
      H16637   Vascular cell adhesion molecule 1   0.034   .005   0.49  
      H97778   E-cadherin   0.039   .006   0.48  
      N64384
 		 Integrin alpha X (CD11C)
 		 0.025
 		 .003
 		 0.32
 

False discovery rate (FDR) corresponds to the expected proportion of falsely called genes among the genes declared to be differentially expressed. RAWP corresponds to the permutation-based unadjusted P value.

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