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Table 1 Top 20 3D gene clusters with smallest p-value using intrachromosomal Hi-C data

From: GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data

Name Genes Penalty p-Value
HOXC HOTAIR_2, HOTAIR_3, HOXC10, HOXC11, HOXC12, HOXC13, HOXC4, HOXC5, HOXC6, HOXC8, HOXC9 0.006 1·10−7
OR OR5AP2, OR5AR1, OR5M1, OR5M10, OR5M11, OR5M3, OR5M8, OR5M9, OR5R1, OR8K1, OR8U1, OR9G1, OR9G 0 1·10−7
IGHV IGHV3-11, IGHV3-13, IGHV3-20, IGHV3-21, IGHV3-23, IGHV3-30, IGHV3-33, IGHV3-35, IGHV3-64D, IGHV3-7 0 1·10−7
KRTAP KRTAP13-1, KRTAP13-2, KRTAP13-3, KRTAP13-4, KRTAP15-1, KRTAP24-1, KRTAP26-1, KRTAP27-1 0 1·10−7
TAS2R TAS2R14, TAS2R19, TAS2R20, TAS2R31, TAS2R46, TAS2R50 0 3.70·10−6
OR OR2A12, OR2A14, OR2A25, OR2A5 0 9.09·10−5
ZSCAN4 NKAPL, ZKSCAN3, ZKSCAN4, ZSCAN26 0.006 0.00015
TRAV TRAV12-1, TRAV12-2, TRAV12-3, TRAV13-1, TRAV13-2, TRAV17, TRAV18, TRAV19, TRAV22, TRAV23DV6, TRAV5, TRAV8-1, TRAV8-3, TRAV9-2 0 0.00037
OR OR5AC1, OR5H1, OR5H14 0 0.00037
IGHV + IGHV1-18, IGHV1-24, IGHV1-3 0 0.00037
BTN3 + BTN3A1, BTN3A2, BTN3A3 0 0.00037
(unnamed) GTF2A1L, STON1, STON1-GTF2A1L 0 0.00037
CYP3A CYP3A4, CYP3A43, CYP3A5, CYP3A7, CYP3A7-CYP3A51P 0.028 0.00037
(unnamed) ADGRE1, C3, CD70, GPR108, TNFSF14, TRIP10, VAV1 0.057 0.00047
ZNF CCDC106, FIZ1, U2AF2, ZNF524, ZNF580, ZNF784, ZNF865 0.097 0.00110
OR OR8B12, OR8B4, OR8B8 0.012 0.00376
KIR KIR2DL1, KIR2DL3, KIR2DL4, KIR2DS4, KIR3DL1, KIR3DL2, KIR3DL3 0.179 0.00243
MMP MMP12, MMP13, MMP3 0.035 0.00486
TSPY + TSPYL1, TSPYL4 0 0.00504
SIGLEC + SIGLEC12, SIGLEC8 0 0.00504
  1. Clusters that can be found as split sub-clusters in the 1D results are marked by an asterisk. Those completely absent in the 1D results are marked by a plus