Table 2.

Early differentiation genes: top 50 differentially expressed genes in comparison of CD19-enriched tonsil BCs and CD138-enriched tonsil PCs

Accession no.SymbolFunctionQuantitative gene expression
TBCsTPCsBPCs
U60519 CASP10 Apoptosis − ++ 
X53586 ITGA6 Adhesion − ++ 
U04735 STCH Chaperone ++ ++ 
L13689 BMI1 Transcription; repressor; PcG ++ +++ 
L34657 PECAM1 Adhesion ++ +++ 
U52682 IRF4 Transcription; IRF family +++ +++ 
M31627 XBP1 Transcription; bZip family +++ ++++ ++++ 
AB000410 OGG1 DNA glycosylase − − 
D87432 SLC7A6 Solute transporter − − 
J04101 ETS1 Transcription; etsfamily − −  
L38820 CDID Immunity − − 
M28827 CDIC Immunity − − 
M55542 GBP1 Signaling; GTP binding − − 
M81182 ABCD3 ABC transporter − − 
M85085 CSTF2 mRNA cleavage stimulating factor − −  
U74612 FOXM1 Transcription; fork-head family − −  
U84720 RAE1 RNA export − −  
V00574 HRAS Signaling; GTP-binding protein − −  
X02910 TNF Signaling; TNFα − −  
X63741 EGR3 Transcription;egr family − −  
X93512 TERF2 Telomere repeat binding protein − −  
Z36714 CCNF Cell cycle; cyclin F − −  
AB000409 MNK1 Signaling; kinase − 
M33308 VCL Cytoskeleton − ++ 
D16480 HADHA Mitochondrial oxidation ++ − − 
M63488 RPA1 DNA replication/repair ++ − − 
U03911 MSH2 DNA repair ++ − − 
U69108 TRAF5 Signaling; TNFR-associated protein ++ − −  
X12517 SNRPC mRNA splicing ++ − −  
X52056 SPI1 Transcription; ets family ++ − −  
X68149 BLR1 Signaling; cxc receptor ++ − −  
X74301 CIITA Transcription; adaptor ++ − −  
X75042 REL Transcription; rel/dorsal family ++ − −  
L00058 MYC Transcription; bHLHZip ++ − ++  
M36067 LIG1 DNA ligase ++ +  
M82882 ELF1 Transcription; ets family ++ +  
S76617 BLK Signaling; kinase ++ +  
U47414 CCNG2 Cell cycle; cyclin G ++ +  
U61167 SH3D1B Unknown; SH3-containing protein ++ +  
X61587 ARHG Signaling; Rho G ++ +  
Z35278 RUNX3 Transcription; contains runt domain ++ +  
U89922 LTB Signaling; TNF-c ++++ +  
M34458 LMNB1 Cytoskeletal matrix +++ −  
U90651 EED Transcription; repression; PcG +++ +  
X69111 ID3 Transcription; repression; bHLH +++ +  
X52425 IL4R Signaling; cytokine receptor +++ ++ −  
Z35227 ARHH Signaling; Rho H +++ ++ +  
U89922 LTB Signaling; TNF-c ++++ +  
U05340 CDC20 Cell cycle; activator of APC ++++ ++ −  
X66079 SPIB Transcription;ets family ++++ ++ − 
Accession no.SymbolFunctionQuantitative gene expression
TBCsTPCsBPCs
U60519 CASP10 Apoptosis − ++ 
X53586 ITGA6 Adhesion − ++ 
U04735 STCH Chaperone ++ ++ 
L13689 BMI1 Transcription; repressor; PcG ++ +++ 
L34657 PECAM1 Adhesion ++ +++ 
U52682 IRF4 Transcription; IRF family +++ +++ 
M31627 XBP1 Transcription; bZip family +++ ++++ ++++ 
AB000410 OGG1 DNA glycosylase − − 
D87432 SLC7A6 Solute transporter − − 
J04101 ETS1 Transcription; etsfamily − −  
L38820 CDID Immunity − − 
M28827 CDIC Immunity − − 
M55542 GBP1 Signaling; GTP binding − − 
M81182 ABCD3 ABC transporter − − 
M85085 CSTF2 mRNA cleavage stimulating factor − −  
U74612 FOXM1 Transcription; fork-head family − −  
U84720 RAE1 RNA export − −  
V00574 HRAS Signaling; GTP-binding protein − −  
X02910 TNF Signaling; TNFα − −  
X63741 EGR3 Transcription;egr family − −  
X93512 TERF2 Telomere repeat binding protein − −  
Z36714 CCNF Cell cycle; cyclin F − −  
AB000409 MNK1 Signaling; kinase − 
M33308 VCL Cytoskeleton − ++ 
D16480 HADHA Mitochondrial oxidation ++ − − 
M63488 RPA1 DNA replication/repair ++ − − 
U03911 MSH2 DNA repair ++ − − 
U69108 TRAF5 Signaling; TNFR-associated protein ++ − −  
X12517 SNRPC mRNA splicing ++ − −  
X52056 SPI1 Transcription; ets family ++ − −  
X68149 BLR1 Signaling; cxc receptor ++ − −  
X74301 CIITA Transcription; adaptor ++ − −  
X75042 REL Transcription; rel/dorsal family ++ − −  
L00058 MYC Transcription; bHLHZip ++ − ++  
M36067 LIG1 DNA ligase ++ +  
M82882 ELF1 Transcription; ets family ++ +  
S76617 BLK Signaling; kinase ++ +  
U47414 CCNG2 Cell cycle; cyclin G ++ +  
U61167 SH3D1B Unknown; SH3-containing protein ++ +  
X61587 ARHG Signaling; Rho G ++ +  
Z35278 RUNX3 Transcription; contains runt domain ++ +  
U89922 LTB Signaling; TNF-c ++++ +  
M34458 LMNB1 Cytoskeletal matrix +++ −  
U90651 EED Transcription; repression; PcG +++ +  
X69111 ID3 Transcription; repression; bHLH +++ +  
X52425 IL4R Signaling; cytokine receptor +++ ++ −  
Z35227 ARHH Signaling; Rho H +++ ++ +  
U89922 LTB Signaling; TNF-c ++++ +  
U05340 CDC20 Cell cycle; activator of APC ++++ ++ −  
X66079 SPIB Transcription;ets family ++++ ++ − 

Quantitative gene expression (QGE) was defined as being at 1 of 5 levels. A gene was “−” if all the samples in the group had an absent absolute call (AC), “+” when all samples had present AC and average difference call (AD) < 1000, “++” when all samples had present AC and AD between 1000 and 5000, “+++” when all samples had present AC and AD between 5000 and 10 000, and “++++” when all samples had present AC and AD > 10 000. Up-regulated LDGs (n = 7) in the tonsil BC to tonsil PC transition are listed first. A hierarchy in the listing of genes was established such that QGE (5 expression levels) increases from top to bottom and from left to right for up-regulated genes and increases from top to bottom and decreases from left to right for down-regulated genes. Although the expression patterns of bone marrow PCs were not used to derive the list of EDGs, the gene expression levels in these cells are provided for reference.

Accession numbers are GenBank accession numbers corresponding to the Affymetrix GeneChip probe set for the given gene. Symbols are HUGO-approved gene symbols. TBCs indicates CD19-enriched tonsil BCs; TPCs, CD138-enriched tonsil PCs; BPCs, CD138-enriched bone marrow PCs.

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