Table S2.

Gene ontology analysis of class 2 genes harboring TSS-proximal translocation junctions

GO biological process completeREFLIST n = 22,320Class 2 genes with junctions within 2 kb of the TSSExpected, nP value
Xrcc4−/− p53−/− Chr15-Myc-sgRNA NSPC experiments (n = 221 class 2 genes with junctions located within 2 kb of the TSS)
 Metabolic process (GO:0008152)*7,85811877.811.85E-04
 Cellular metabolic process (GO:0044237)*6,83310667.663.76E-04
 Primary metabolic process (GO:0044238)*7,07910870.096.28E-04
 Organic substance metabolic process (GO:0071704)*7,36711072.941.41E-03
 Macromolecule metabolic process (GO:0043170)*5,8929058.341.93E-02
 Cellular macromolecule metabolic process (GO:0044260)*5,2828352.32.02E-02
ATM−/− R26I-SceI-GR c-Myc25xI-SceI NSPC experiments (n = 277 class 2 genes with junctions located within 2 kb of the TSS)
 Metabolic process (GO:0008152)*7,85815397.526.12E-08
 Cellular metabolic process (GO:0044237)*6,83313784.83.40E-07
 Organic substance metabolic process (GO:0071704)*7,36714491.434.35E-07
 Primary metabolic process (GO:0044238)*7,07914087.854.64E-07
 Cellular macromolecule metabolic process (GO:0044260)*5,28211265.553.43E-06
 Macromolecule metabolic process (GO:0043170)*589212073.126.62E-06
 Cellular process (GO:0009987)*13,249208164.432.12E-04
 Organelle organization (GO:0006996)*2,4945830.951.46E-02
 Heterocycle metabolic process (GO:0046483)*3,5267443.761.83E-02
 Organic cyclic compound metabolic process (GO:1901360)*3,7517746.552.44E-02
 Nucleobase-containing compound metabolic process (GO:0006139)*3,3887142.053.34E-02
 Cellular component organization (GO:0016043)*4,1218251.143.47E-02
 Nitrogen compound metabolic process (GO:0006807)*4,1898351.993.48E-02
 Cellular component organization or biogenesis (GO:0071840)*4,2608452.873.59E-02
 Cellular protein metabolic process (GO:0044267)*2,7186033.734.83E-02
Xrcc4−/− p53−/− Chr12-sgRNA-1 NSPC experiments (n = 306 class 2 genes with junctions located within 2 kb of the TSS
 Cellular metabolic process (GO:0044237)*6,83313893.685.26E-04
 Cellular macromolecule metabolic process (GO:0044260)*5,28210972.411.28E-02
 Phosphate-containing compound metabolic process (GO:0006796)1,6124622.11.58E-02
 Primary metabolic process (GO:0044238)*7,07913597.052.74E-02
 Organic substance metabolic process (GO:0071704)*7,3671391013.13E-02
 Phosphorus metabolic process (GO:0006793)1,6564622.73.20E-02
 Metabolic process (GO:0008152)*7,858146107.733.43E-02
 Regulation of organelle organization (GO:0033043)1,02133144.25E-02
ATM−/− c-Myc25xI-SceI B-cell experiments (n = 416 class 2 genes with junctions located within 2 kb of the TSS (31)
 Cellular metabolic process (GO:0044237)*6,833224127.355.38E-19
 Metabolic process (GO:0008152)*7,858244146.461.39E-18
 Organic substance metabolic process (GO:0071704)*7,367228137.314.11E-16
 Cellular macromolecule metabolic process (GO:0044260)*5,28218398.455.45E-16
 Primary metabolic process (GO:0044238)*7,079220131.942.67E-15
 Macromolecule metabolic process (GO:0043170)*5,892192109.823.26E-14
 Cellular nitrogen compound metabolic process (GO:0034641)3,90014172.694.34E-12
 Cellular process (GO:0009987)*13,249323246.931.76E-11
 Nitrogen compound metabolic process (GO:0006807)*4,18914578.075.19E-11
 Nucleobase-containing compound metabolic process (GO:0006139)*3,38812163.153.27E-09
 Heterocycle metabolic process (GO:0046483)*3,52612265.722.21E-08
 Cellular aromatic compound metabolic process (GO:0006725)3,55912266.334.14E-08
 Cellular macromolecule Biosynthetic process (GO:0034645)2,5919748.291.20E-07
 Macromolecule biosynthetic process (GO:0009059)2,6159748.742.01E-07
 Nucleic acid metabolic process (GO:0090304)2,97910655.522.07E-07
 Cellular protein metabolic process (GO:0044267)*2,7189950.663.25E-07
 Gene expression (GO:0010467)2,88510353.773.63E-07
 Cellular component organization or biogenesis (GO:0071840)*4,26013579.44.89E-07
 Organic cyclic compound metabolic process (GO:1901360)*3,75112369.916.17E-07
 Cellular biosynthetic process (GO:0044249)3,27011160.951.03E-06
 Negative regulation of biological process (GO:0048519)4,13313177.031.09E-06
 Cellular nitrogen compound biosynthetic process (GO:0044271)2,5089246.741.37E-06
 Negative regulation of cellular process (GO:0048523)3,81112371.031.71E-06
 Biosynthetic process (GO:0009058)3,44611464.232.47E-06
 Biological process (GO:0008150)20,668412385.215.40E-06
 Organic substance biosynthetic process (GO:1901576)3,37111162.836.13E-06
 RNA metabolic process (GO:0016070)2,5729047.942.37E-05
 Organelle organization (GO:0006996)*2,4948846.482.52E-05
 Cellular component organization (GO:0016043)*4,12112676.812.87E-05
 Protein metabolic process (GO:0019538)3,36210862.664.48E-05
 Regulation of primary metabolic process (GO:0080090)4,89714191.271.10E-04
 Positive regulation of macromolecule metabolic process (GO:0010604)2,5378747.281.19E-04
 Regulation of cellular metabolic process (GO:0031323)5,06214494.351.54E-04
 Regulation of metabolic process (GO:0019222)5,686157105.981.80E-04
 Regulation of macromolecule metabolic process (GO:0060255)4,89314091.21.91E-04
 Macromolecular complex subunit organization (GO:0043933)1,7376632.372.36E-04
 Negative regulation of cellular metabolic process (GO:0031324)2,0587438.362.82E-04
 Negative regulation of metabolic process (GO:0009892)2,2857942.594.61E-04
 Translation (GO:0006412)271215.055.26E-04
 Negative regulation of macromolecule metabolic process (GO:0010605)2,0487238.171.07E-03
 Regulation of nitrogen compound metabolic process (GO:0051171)3,50710665.361.51E-03
 Peptide biosynthetic process (GO:0043043)291215.421.67E-03
 Ribonucleoprotein complex biogenesis (GO:0022613)295215.52.08E-03
 Regulation of macromolecule Biosynthetic process (GO:0010556)3,26910060.932.18E-03
 Chromatin organization (GO:0006325)5543010.332.23E-03
 Positive regulation of metabolic process (GO:0009893)3,1729759.123.56E-03
 Positive regulation of cellular metabolic process (GO:0031325)2,7008650.323.67E-03
 Peptide metabolic process (GO:0006518)369236.885.52E-03
 Cellular component biogenesis (GO:0044085)1,7486232.586.81E-03
 Negative regulation of macromolecule biosynthetic process (GO:0010558)1,2284822.891.03E-02
 Regulation of biosynthetic process (GO:0009889)3,49710265.181.46E-02
 Heterocycle biosynthetic process (GO:0018130)2,1757140.541.95E-02
 Negative regulation of biosynthetic process (GO:0009890)1,3034924.292.29E-02
 Response to stress (GO:0006950)2,5257947.062.37E-02
 Amide biosynthetic process (GO:0043604)347216.472.62E-02
 Nucleobase-containing compound biosynthetic process (GO:0034654)2,1136939.382.74E-02
 Positive regulation of macromolecule biosynthetic process (GO:0010557)1,5465528.812.79E-02
 Homeostasis of number of cells (GO:0048872)215164.013.14E-02
 Regulation of nucleobase-containing compound metabolic process (GO:0019219)3,2899661.33.16E-02
 Protein transport (GO:0015031)9834018.323.26E-02
 Regulation of cellular macromolecule biosynthetic process (GO:2000112)3,1719359.13.86E-02
 Immune system process (GO:0002376)1,5295428.54.25E-02
 Aromatic compound biosynthetic process (GO:0019438)2,1837040.694.28E-02
 Establishment of protein localization (GO:0045184)1,0714219.964.55E-02
  • Gene ontology (GO) analyses were performed by the Protein Analysis Through Evolutionary Relationships (PANTHER) classification system (43, 44). Gene numbers analyzed for each experiment are indicated. Analysis Type used: PANTHER Overrepresentation Test (release 20150430); annotation version and release date: GO Ontology database, 2015-08-06; Bonferroni correction: true; reference list (REFLIST): Mus musculus (all genes in database).

  • * Shared GO terms across experiments.