Table 2.

Genome annotation enrichment clusters

AnnotationEnrichment Score: 2.098930503473424
cluster 1TermPGenes
GO:0045657: positive regulation of monocyte differentiation4.62E−04JUN, CSF1, ACIN1
GO:0045655: regulation of monocyte differentiation9.16E−04JUN, CSF1, ACIN1
GO:0002763: positive regulation of myeloid leukocyte differentiation0.001361426IKZF1, JUN, CSF1, ACIN1
GO:0045639: positive regulation of myeloid cell differentiation0.007937827IKZF1, JUN, CSF1, ACIN1
GO:0045637: regulation of myeloid cell differentiation0.011372639HIST4H4, IKZF1, JUN, CSF1, ACIN1
GO:0002761: regulation of myeloid leukocyte differentiation0.014424008IKZF1, JUN, CSF1, ACIN1
AnnotationEnrichment score: 1.600658678135878
cluster 2TermPGenes
Topological domain: Lumenal0.002991392TCIRG1, GCNT4, TPST2, ST6GAL2, GOLT1B, IGF2R, LMAN2L, CSF1, ASPHD2, GALNT4, EXT1, ABO, PPAP2B, MOXD1
Golgi apparatus0.011871437TPST2, GCNT4, ST6GAL2, AP1G2, GOLT1B, LMAN2L, GALNT4, TMF1, SGSM1, TNKS, PTGFRN, EXT1, ABO, PPAP2B, GOLGA4
AnnotationEnrichment score: 1.5412837811532563
cluster 3TermPGenes
GO:0030099: myeloid cell differentiation0.001081276DNASE2, CEBPA, CEBPE, CSF1, ACIN1, KLF1, FLVCR1
GO:0030225: macrophage differentiation0.004134616CEBPA, CEBPE, CSF1
GO:0030097: hemopoiesis0.009664139DNASE2, CEBPA, KLF6, CEBPE, IKZF1, CSF1, ACIN1, KLF1, FLVCR1
GO:0030218: erythrocyte differentiation0.016399444DNASE2, ACIN1, KLF1, FLVCR1
GO:0048534: hemopoietic or lymphoid organ development0.016484328DNASE2, CEBPA, KLF6, CEBPE, IKZF1, CSF1, ACIN1, KLF1, FLVCR1
GO:0002520: immune system development0.022674988DNASE2, CEBPA, KLF6,CEBPE, IKZF1, CSF1, ACIN1, KLF1, FLVCR1
GO:0034101: erythrocyte homeostasis0.023193847DNASE2, ACIN1, KLF1, FLVCR1
GO:0048872: homeostasis of number of cells0.036577024DNASE2, CSF1, ACIN1, KLF1, FLVCR1
AnnotationEnrichment score: 1.4825623926872973
cluster 4TermPGenes
GO:0046983: protein dimerization activity0.011842272CEBPA, CHKA, IKZF1, CEBPE, CSF1, HPS4, EEA1, RRAGC, ABCG8, CDH13, ABCG5, JUN, UBA3,GYS2, EXT1
GO:0042802: identical protein binding0.041495104CEBPA, CHKA, CEP72, CEBPE, CSF1, HPS4, FBP1, FHL2, EEA1, GUCY2D, CDH13, DOK2,GYS2, EXT1, PHLDA3
AnnotationEnrichment score: 1.3866597881487874
cluster 5TermPGenes
GO:0034637: cellular carbohydrate biosynthetic process0.001691251GLT25D1, FBP1, GYS2, FBP2, EXT1, PPARGC1A
GO:0016051: carbohydrate biosynthetic process0.01096541GLT25D1, FBP1, GYS2, FBP2, EXT1, PPARGC1A
GO:0033692: cellular polysaccharide biosynthetic process0.041446472GLT25D1, GYS2, EXT1
  • NOTE: Table 2 shows genome annotation enrichment clusters for ALL-associated genes. We performed GO and KEGG pathway annotation enrichment analysis using DAVID (17, 18) for gene scores generated from GWA results. We find that five annotation clusters achieved a significant enrichment score (greater than 1.3). Significant annotations (P < 0.05) within these clusters include hematopoiesis, immune system development, erythrocyte differentiation, and regulation of monocyte differentiation. Gene names that are bold represent genes that appear in significant HotNet2 gene subnetworks in this study (Fig. 1; Supplementary Figs. S2 and S3).