Supplementary Materials

Activation of proto-oncogenes by disruption of chromosome neighborhoods

Denes Hnisz, Abraham S. Weintraub, Daniel S. Day, Anne-Laure Valton, Rasmus O. Bak, Charles H. Li, Johanna Goldmann, Bryan R. Lajoie, Zi Peng Fan, Alla A. Sigova, Jessica Reddy, Diego Borges-Rivera, Tong Ihn Lee, Rudolf Jaenisch, Matthew H. Porteus, Job Dekker, Richard A. Young

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S16
  • Captions for tables S1 to S13
  • References
Table S1
Summary statistics of the Jurkat SMC1 ChIA-PET data
Table S2
SMC1 ChIA-PET interactions
Table S3
T-ALL Pathogenesis Genes
Table S4
Gene expression (RPKM) values in Jurkat cells
Table S5
Deletions in T-ALL genomes overlapping insulated neighborhood boundaries
Table S6
5C primers
Table S7
5C summary statistics
Table S8
Constitutive neighborhoods across three cell types
Table S9
ICGC datasets
Table S10
Somatic mutations in constitutive neighborhood boundary sites
Table S11
GO-analysis of genes with neighborhood boundary mutations
Table S12
Candidate proto-oncogenes extracted from the Cancer Gene Census
Table S13
GEO accession IDs of the datasets used in this study