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