Table 1

Gene ontology (GO) terms represented among BCL6 target genes

GC-specific genesCommon genesDLBCL-specific genesGO term
3 (0)* 2 (1)† 1 (1)† GO:0043038 amino acid activation 
3 (0)* 2 (1)† 1 (1)† GO:0006418 tRNA aminoacylation for protein translation 
3 (0)* 2 (1)† 4 (1)† GO:0006399 tRNA metabolic process 
6 (1)* 5 (3)† 9 (4)† GO:0034660 ncRNA metabolic process 
3 (0)* 2 (1)† 1 (1)† GO:0043039 tRNA aminoacylation 
0 (0)† 3 (0)* 0 (0)† GO:0045739 positive regulation of DNA repair 
0 (0)† 4 (1)* 1 (1)† GO:0006282 regulation of DNA repair 
4 (2)† 16 (7)* 12 (8)† GO:0006511 ubiquitin-dependent protein catabolic process 
4 (2)† 17 (8)* 12 (9)† GO:0030163 protein catabolic process 
4 (2)† 16 (7)* 12 (8)† GO:0044257 cellular protein catabolic process 
8 (4)† 22 (13)* 24 (15)† GO:0043285 biopolymer catabolic process 
4 (2)† 16 (7)* 12 (8)† GO:0043632 modification-dependent macromolecule catabolic process 
4 (2)† 16 (7)* 12 (8)† GO:0051603 proteolysis involved in cellular protein catabolic process 
3 (2)† 13 (5)* 8 (6)† GO:0051438 regulation of ubiquitin-protein ligase activity 
3 (2)† 13 (5)* 8 (6)† GO:0051340 regulation of ligase activity 
3 (1)† 11 (4)* 8 (5)† GO:0051436 negative regulation of ubiquitin-protein ligase activity during mitotic cell cycle 
0 (0)† 4 (1)* 3 (1)† GO:0009303 rRNA transcription 
0 (0)† 1 (1)† 7 (2)* GO:0000910 cytokinesis 
0 (0)† 1 (1)† 7 (2)* GO:0051301 cell division 
6 (3)† 12 (10)† 25 (12)* GO:0022403 cell cycle phase 
3 (1)† 8 (4)† 13 (5)* GO:0007050 cell cycle arrest 
3 (1)† 7 (3)† 10 (4)* GO:0007067 mitosis 
3 (1)† 8 (4)† 10 (4)* GO:0000087 M phase of mitotic cell cycle 
5 (2)† 10 (7)† 18 (8)* GO:0000279 M phase 
6 (4)† 20 (12)† 26 (14)* GO:0000278 mitotic cell cycle 
8 (4)† 20 (12)† 30 (14)* GO:0034984 cellular response to DNA damage stimulus 
9 (5)† 24 (15)† 33 (17)* GO:0051716 cellular response to stimulus 
8 (4)† 22 (14)† 32 (16)* GO:0033554 cellular response to stress 
10 (4)† 20 (14)† 28 (16)* GO:0006366 transcription from RNA polymerase II promoter 
6 (2)† 10 (7)† 18 (8)* GO:0006414 translational elongation 
0 (0)† 0 (0)† 3 (0)* GO:0018211 peptidyl-tryptophan modification 
0 (0)† 0 (0)† 3 (0)* GO:0018317 protein amino acid C-linked glycosylation via tryptophan 
0 (0)† 0 (0)† 3 (0)* GO:0018406 protein amino acid C-linked glycosylation via 2′-alpha-mannosyl-L-tryptophan 
0 (0)† 0 (0)† 3 (0)* GO:0035269 protein amino acid O-linked mannosylation 
0 (0)† 0 (0)† 3 (0)* GO:0035268 protein amino acid mannosylation 
2 (0)† 1 (1)† 4 (1)* GO:0043631 RNA polyadenylation 
5 (3)† 16 (11)† 26 (13)* GO:0034622 cellular macromolecular complex assembly 
9 (4)† 23 (14)† 30 (16)* GO:0044265 cellular macromolecule catabolic process 
5 (4)† 18 (12)† 26 (14)* GO:0034621 cellular macromolecular complex subunit organization 
11 (7)† 27 (21)† 39 (24)* GO:0022607 cellular component assembly 
11 (7)† 30 (21)† 39 (25)* GO:0043933 macromolecular complex subunit organization 
11 (6)† 27 (20)† 39 (23)* GO:0065003 macromolecular complex assembly 
2 (0)† 0 (2)† 7 (2)* GO:0045333 cellular respiration 
0 (1)† 5 (2)† 7 (2)* GO:0006730 one-carbon compound metabolic process 
9 (7)† 25 (21)† 45 (24)* GO:0006996 organelle organization 
GC-specific genesCommon genesDLBCL-specific genesGO term
3 (0)* 2 (1)† 1 (1)† GO:0043038 amino acid activation 
3 (0)* 2 (1)† 1 (1)† GO:0006418 tRNA aminoacylation for protein translation 
3 (0)* 2 (1)† 4 (1)† GO:0006399 tRNA metabolic process 
6 (1)* 5 (3)† 9 (4)† GO:0034660 ncRNA metabolic process 
3 (0)* 2 (1)† 1 (1)† GO:0043039 tRNA aminoacylation 
0 (0)† 3 (0)* 0 (0)† GO:0045739 positive regulation of DNA repair 
0 (0)† 4 (1)* 1 (1)† GO:0006282 regulation of DNA repair 
4 (2)† 16 (7)* 12 (8)† GO:0006511 ubiquitin-dependent protein catabolic process 
4 (2)† 17 (8)* 12 (9)† GO:0030163 protein catabolic process 
4 (2)† 16 (7)* 12 (8)† GO:0044257 cellular protein catabolic process 
8 (4)† 22 (13)* 24 (15)† GO:0043285 biopolymer catabolic process 
4 (2)† 16 (7)* 12 (8)† GO:0043632 modification-dependent macromolecule catabolic process 
4 (2)† 16 (7)* 12 (8)† GO:0051603 proteolysis involved in cellular protein catabolic process 
3 (2)† 13 (5)* 8 (6)† GO:0051438 regulation of ubiquitin-protein ligase activity 
3 (2)† 13 (5)* 8 (6)† GO:0051340 regulation of ligase activity 
3 (1)† 11 (4)* 8 (5)† GO:0051436 negative regulation of ubiquitin-protein ligase activity during mitotic cell cycle 
0 (0)† 4 (1)* 3 (1)† GO:0009303 rRNA transcription 
0 (0)† 1 (1)† 7 (2)* GO:0000910 cytokinesis 
0 (0)† 1 (1)† 7 (2)* GO:0051301 cell division 
6 (3)† 12 (10)† 25 (12)* GO:0022403 cell cycle phase 
3 (1)† 8 (4)† 13 (5)* GO:0007050 cell cycle arrest 
3 (1)† 7 (3)† 10 (4)* GO:0007067 mitosis 
3 (1)† 8 (4)† 10 (4)* GO:0000087 M phase of mitotic cell cycle 
5 (2)† 10 (7)† 18 (8)* GO:0000279 M phase 
6 (4)† 20 (12)† 26 (14)* GO:0000278 mitotic cell cycle 
8 (4)† 20 (12)† 30 (14)* GO:0034984 cellular response to DNA damage stimulus 
9 (5)† 24 (15)† 33 (17)* GO:0051716 cellular response to stimulus 
8 (4)† 22 (14)† 32 (16)* GO:0033554 cellular response to stress 
10 (4)† 20 (14)† 28 (16)* GO:0006366 transcription from RNA polymerase II promoter 
6 (2)† 10 (7)† 18 (8)* GO:0006414 translational elongation 
0 (0)† 0 (0)† 3 (0)* GO:0018211 peptidyl-tryptophan modification 
0 (0)† 0 (0)† 3 (0)* GO:0018317 protein amino acid C-linked glycosylation via tryptophan 
0 (0)† 0 (0)† 3 (0)* GO:0018406 protein amino acid C-linked glycosylation via 2′-alpha-mannosyl-L-tryptophan 
0 (0)† 0 (0)† 3 (0)* GO:0035269 protein amino acid O-linked mannosylation 
0 (0)† 0 (0)† 3 (0)* GO:0035268 protein amino acid mannosylation 
2 (0)† 1 (1)† 4 (1)* GO:0043631 RNA polyadenylation 
5 (3)† 16 (11)† 26 (13)* GO:0034622 cellular macromolecular complex assembly 
9 (4)† 23 (14)† 30 (16)* GO:0044265 cellular macromolecule catabolic process 
5 (4)† 18 (12)† 26 (14)* GO:0034621 cellular macromolecular complex subunit organization 
11 (7)† 27 (21)† 39 (24)* GO:0022607 cellular component assembly 
11 (7)† 30 (21)† 39 (25)* GO:0043933 macromolecular complex subunit organization 
11 (6)† 27 (20)† 39 (23)* GO:0065003 macromolecular complex assembly 
2 (0)† 0 (2)† 7 (2)* GO:0045333 cellular respiration 
0 (1)† 5 (2)† 7 (2)* GO:0006730 one-carbon compound metabolic process 
9 (7)† 25 (21)† 45 (24)* GO:0006996 organelle organization 

The first 3 columns list the number of targets per GO term present among GC-specific, in common between GC and DLBCL and DLBCL-specific genes. The values in parentheses denote the expected number of genes per GO term for each category (ie, GC, common, DLBCL).

*

The numbers show significant enrichment versus expected (as demonstrated in the heatmap color code in Figure 1A).

†

The numbers are nonsignificant.

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