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Table 1 Cytogenetic band(s) where RER regions common to breast tumors and breast cancer cell lines are located

From: Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer

Cytogenetic location Size (Mb) Number of significant TCSs (tumor/cell line) Number of other significantly correlated genes (tumor/cell line) Genes in RER regions with significant TCSs Gene expression (tumor versus normal)
6p22.2 0.89 3/34 14/28 C6orf62, GMNN, HIST1H4C/Histone gene cluster, ZSCAN16, GPX5, OR2W1, OR2J3, OR2N1P, OR12D2, OR10C1, MOG Up
6q23.2-q23.3 3.43 12/3 26/10 TAAR5, TAAR3, VNN3, IFNGR1, HEBP2, ABRACL, HECA, VTA1, PEX3, FUCA2, LTV1, SHPRH, PPIL4, RMND1, C6orf211 Down
6q25.1-q25.3 6.71 12/3 26/7 RP23-468K3.1, RP3-527B10.1, OPRM1 Down
8p11.21-q11.23 13.41 6/6 17/8 TM2D2, GOLGA7, KAT6A, AP3M2, IKBKB, POLB, VDAC3, SLC20A2, SMIM19, MCM4, MRPL15 Down
8q21.13-q21.3 10.54 32/6 33/11 NBN, OTUD6B, RAD54B, KIAA1429, ESRP1, INTS8, PLEKHF2, MTERFD1, PTDSS1, MTDH, HRSP12, AP003355.2, VPS13B, ANKRD46, UBR5, AZIN1, ATP6V1C1, SLC25A32, TTC35, TAF2, MRPL13, DERL1, ATAD2, WDYHV1, TRMT12, RNF139/KCNB2, STAU2, FAM164A, STMN2, FAM82B, MMP16 No change
8q22.1-q23.1 11.99 32/11 33/3 NBN, OTUD6B, RAD54B, KIAA1429, ESRP1, INTS8, PLEKHF2, MTERFD1, PTDSS1, MTDH, RPL30, HRSP12, AP003355.2, NIPAL2, VPS13B, COX6C, SPAG1, RNF19A, ANKRD46, UBR5, AZIN1, ATP6V1C1, FZD6, SLC25A32, EMC2, TAF2, MRPL13, DERL1, ATAD2, WDYHV1, TRMT12, RNF139 No change
9p13.3 1.13 2/6 20/11 NOL6, SIGMAR1, KIAA1045, DNAJB5, RUSC2, CD72, SIT1, CA9 No change
10p13-p12.31 6.71 5/3 22/10 UPF2, CDC123, HSPA14, RPP38, NMT2, RSU1, STAM Down
10q26.11-q26.13 6.34 3/5 21/10 BAG3, C10orf119, SEC23IP, BRWD2, PLEKHA1, IKZF5 No change
11q12.3-q13.1 0.75 5/2 27/9 C11orf48, WDR74, COX8A, OTUB1, MACROD1, NUDT22, RPS6KA4 Up
11q13.2 0.36 6/2 18/9 KAT5, FIBP, CCDC85B, SART1, SF3B2, YIF1A , SPTBN2, C11orf80 Up
12q21.31-q21.33 10.39 2/4 17/12 RAB21, PPP1R12A , NTS, MGAT4C, DCN, EEA1 Down
16p13.3 2.16 23/23 33/22 AXIN1, TMEM8A, NME4, RAB11FIP3, PIGQ, RAB40C, LA16c-398G5.2, WDR90, RHOT2, WDR24, METRN, FAM173A, CCDC78, NARFL, IFT140, NME3, MRPS34, HAGH, NDUFB10, GFER, NTHL1, TRAF7, MLST8, E4F1, GNG13, LMF1, CACNA1H, TPSG1, TPSD1, UBE2I, BAIAP3, PGP Up
16p13.3 1.45 4/5 16/12 OR1F1, OR2C1, NAA60, ADCY9, TFAP4, DNAJA3, ANKS3, ROGDI, UBN1 Up
16p12.3 0.38 3/2 13/6 KNOP1, GP2, EARS2, NDUFAB1, PALB2 No change
16p11.2 1.36 6/25 22/13 SEZ6L2, TAOK2, HIRIP3, DOC2A, ALDOA, PPP4C, TBX6, MAPK3, CD2BP2, TBC1D10B, ZNF48, ZNF771, ZNF768, ZNF747, ZNF764, ZNF688, ZNF785, PRR14, FBRS, SRCAP, PHKG2, RNF40, ZNF629, BCL7C, CTF1, SETD1A, VKORC1 Up
16q22.1-q22.2 4.9 22/11 71/17 CDH16, NOL3, E2F4, ATP6V0D1, THAP11, PSKH1, DDX28, DUS2L, PRMT7, COG4, VAC14 Down
17p11.2 1.69 17/3 26/6 TOM1L2, LRRC48, LLGL1 Down
17q11.2 0.53 17/4 26/6 UNC119, KIAA0100, SDF2, SUPT6H Up
17q21.2 0.28 17/6 13/9 KRTAP1-3, KRTAP1-1, KRTAP2-4, KRTAP4-9, KRT34, KRT31 No change
17q25.1 0.9 24/4 20/6 KCTD2, GGA3, MRPS7, GRB2 Up
17q25.3 0.58 13/4 18/13 STRA13, RFNG, CSNK1D, SECTM1 Up
22q11.23-q12.1 5.93 5/13 15/20 TRMT2A, P2RX6, TOP3B, PPIL2, IGLV1-40, ZNF280B, ZNF280A, ZDHHC8P, VPREB3, MMP11, UPB1, SEZ6L, CRYBB1 Down
22q12.2-q12.3 1.01 3/2 15/11 INPP5J, PIK3IP1 No change
22q12.3 0.24 3/4 15/12 TMPRSS6, SSTR3, MFNG, GCAT No change
22q13.1-q13.2 1.37 2/6 16/10 CBX6, APOBEC3A, PDGFB, MGAT3, CACNA1I, SGSM3 No change
  1. The RER region size (measured as the first to last significant TCS in the region), the number of genes with significant TCSs in the tumor or cell line data, the number of other genes in the region which have significantly correlated expression with the TCS genes (again for tumors and cell lines), and the list of those genes with significant TCSs. The gene expression of the region in tumors compared with normal samples is also indicated