Table 1.
Individual chromosomal islands of up- or down-regulation.
| expression change | start region | end region | start gene | end gene | potential tumor genes, hereditary CRC, known chromosomal imbalances |
| loss | 1p36.33 | 1p36.32 | TNFRSF18 | ARHGEF16 | amplification of 1p36.33-p32 in CRC [25] // deletion of 13p36.3 in 25% of neuroblastomas and 87% of cell lines [45] // loss of expression and genomic deletion on 1p [17] |
| loss | 1p36.13 | 1p36.11 | PADI1 | DKFZP434L0117 | E2F2 // ID3 // loss of 1p36.1 in CRC [22, 25] // loss of expression and genomic deletion on 1p [17] |
| loss | 1p35.1 | 1p34.3 | HDAC1 | PSMB2 | LCK at 1p35.1 // hereditary CRC at 1p35 (OMIM 114500) // loss of expression and genomic deletion on 1p [17] |
| gain | 1q32.1 | 1q41 | PIGR | DKFZp547M236 | 1q32 amplification involving MDM4 and CNTN2 in malignant gliomas [46] |
| gain | 2p25.3 | 2p24.2 | Hs.8379.0 | VSNL1 | hereditary CRC at 2p25 (OMIM 114500) |
| loss | 2p11.2 | 2q12.1 | MAT2A | MGC11332 | 83% loss of 2p11 in mantle cell lymphoma [47] // loss in mantle cell lymphoma [48] |
| gain | 2q31.3 | 2q32.2 | SSFA2 | NAB1 | hereditary HNPCC3 at 22q31-q33 (OMIM 600258) // familial breast cancer at 2q (OMIM 114480) |
| gain | 2q33.2 | 2q35 | Hs.163603 | AAMP | familial breast cancer at 2q (OMIM 114480) |
| loss | 2q37.3 | 2q37.3 | SCLY | FARP2 | familial breast cancer at 2q (OMIM 114480) |
| gain | 3p25.3 | 3p25.1 | KIAA0121 | CAPN7 | amplification of 3p25.2 in CRC [25] // RAF1 at 3p25.2 // FBLN1 at 3p25.2 |
| gain | 3p25.1 | 3p24.2 | RAFTLIN | THRB | |
| gain | 3p24.2 | 3p23 | FLJ20604 | CLASP2 | |
| loss | 3p21.31 | 3p21.31 | CELSR3 | NPR2L | hereditary HNPCC2 at 3p21.3 (OMIM 609310) // RASFF1 |
| gain | 3p11.1 | 3q13.11 | MGC26717 | ALCAM | frequent 3q11.2-q13.1 amplifications in cervix carcinomas [49] |
| loss | 3q13.13 | 3q21.2 | Hs.23762.0 | ITGB5 | |
| loss | 4p15.32 | 4p14 | LAP3 | Hs.118993 | deletions of 4p14 in CRC [24] // SLIT2 at 4p15 is inactivated by hypermethylation in gliomas [33] // SLIT2 suppresses tumor growth [32] // loss of expression and genomic deletion on 1p [17] |
| loss | 4q13.2 | 4q13.3 | YT521 | CXCL6 | global loss of expression and genomic deletion on 4 [17] |
| loss | 4q21.21 | 4q22.3 | PRKG2 | LIM | transition of follicular B cell lymphoma to diffuse large cell lymphoma accompanied by 4q21-q23 deletions // global loss of expression and genomic deletion on 4 [17] |
| loss | 4q34.1 | 4q35.2 | HPGD | Hs.130535 | deletion of 4q34-q35 in colorectal cancer cell lines [25] // CASP3 at 4q34.3 // global loss of expression and genomic deletion on 4 [17] |
| loss | 5q15 | 5q23.2 | Hs.444378 | Hs.97104 | hereditary colorectal adenoma and carcinoma 1 (CRAC1) (OMIM 601228) at 15q15.3-q221 // APC at 5q21 // loss of expression and genomic deletion on 5q [17] |
| gain | 5q31.1 | 5q31.3 | HTGN29 | Hs.443121 | loss of expression and genomic deletion on 5q [17] |
| loss | 5q31.3 | 5q33.1 | NDFIP1 | FLJ10290 | amplification of 5q32-q34 in prostate cancer [50] // PDGFRB at 5q32 // loss of expression and genomic deletion on 5q [17] |
| gain | 5q33.2 | 5q35.1 | MRPL22 | FBXW1B | amplification of 5q32-q34 in prostate cancer [50] // loss of expression and genomic deletion on 5q [17] |
| gain | 6p25.3 | 6p24.2 | DUSP22 | NEDD9 | amplification of 6p25 in 24% of mantle cell lymphomas [47] // amplification of 6p25 in 75% of prostate cancers [51] |
| loss | 6p22.3 | 6p22.2 | CAP2 | SLC17A4 | most frequent amplification of 6p22.3 in bladder cancer arrayCGH study [52] |
| loss | 6p21.32 | 6p21.32 | PBX2 | RAB2L | |
| gain | 6p21.31 | 6p21.2 | HMGA1 | RNF8 | CDKN1A at 6p21.2 // PIM1 at 6p21.2 |
| gain | 6q23.3 | 6q24.2 | DUFD1 | Hs.12565 | amplification of 6q23-q24 assosicated with short survival [22] |
| gain | 7p22.3 | 7p21.3 | FLJ23471 | ICA1 | hereditary HNPCC4 at 7p22 (gene PMS2) // gain of expression and genomic amplification of 7 [17] |
| gain | 7p21.2 | 7p15.3 | ETV1 | OSBPL3 | amplification of 7p21 in mantle cell lymphomas [47] // amplification of 7p21 in osteosarcoma [53] // gain of expression and genomic amplification of 7 [17] |
| gain | 7p14.3 | 7p13 | LSM5 | NPC1L1 | gain of expression and genomic amplification of 7 [17] |
| loss | 7q11.23 | 7q21.3 | SRCRB4D | CAS1 | amplification of 7q11.1-q12 in metastatic CRC [24] // gain of expression and genomic amplification of 7 [17] |
| gain | 7q31.31 | 7q33 | FAM3C | MGC5242 | prostate cancer aggressiveness linked to 7q32-q33 [54] // gain of expression and genomic amplification of 7 [17] |
| gain | 8q11.23 | 8q21.11 | ATP6V1H | ANKTM1 | amplifications of 8q11-q24 in metastasing CRC [29] // LYN at 8q12.1 // MOS at 8q12.1 // familial breast cancer at 8q11 (OMIM 114480) // amplifications at 8q in CRC [18, 21, 23, 25] // gain of expression and genomic amplification of 8q [17] |
| gain | 8q22.3 | 8q24.22 | TIEG | SLA | amplifications of 8q11-q24 in metastasing CRC [29] // MYC at 8q24.21 // PVT1 at 8q24.21 // amplification of 8q23-q24 in prostate cancer [55]// gain of expression and genomic amplification of 8q [17] |
| loss | 9p21.3 | 9p21.1 | IFNA4 | SMU-1 | loss of 9p21 in CRC [25] // TUBE1 at 9p21 // CDKN2A alias p16INK4A at ??? // frequent deletion of 9p21 in prostate cancer [56] // deletion of 9p21.3 in bladder cancer [57] |
| loss | 9p13.3 | 9p13.3 | BAG1 | OPRS1 | frequent LOH at 9p13-p21 in melanoma [58] |
| loss | 9q21.11 | 9q21.32 | Hs.173519.0 | Hs.522256 | loss of 9q21-q22 in mantle cell lymphoma [59] |
| loss | 9q34.11 | 9q34.11 | FLJ14596 | GPR107 | ABL1 protooncogene at 9q34.12 |
| loss | 10p15.3 | 10p12.2 | Hs.255096 | Hs.57079.0 | frequent LOH of 10p15 in gastric cancer [60] // telomerase repressor at 10q15.1 [61] // deletion of 10p14 in mantle cell lymphoma [47, 59] // OPTN at 10p14 [62] |
| loss | 10q11.21 | 10q11.23 | Hs.173866.0 | MOB | RET at 10q11.21 // LOH in prostate cancer at 10q11.21 [51] |
| loss | 11p15.5 | 11p15.5 | RNH | MUC5AC | hereditary CRC at 11p15.5 / HRAS at 11p15.5 // 11p15.5 methylation-dependent expression silencing and imprinting in phaeochromocytomas [63] |
| gain | 11p15.5 | 11p15.4 | CTSD | SSA1 | CTSD (Cathepsin D) at 11p15.5 // familial breast cancer at 11p15.5 (OMIM 114480) |
| gain | 11p13 | 11p12 | Hs.120054.0 | TRAF6 | WT1 at 11p13 |
| gain | 11p11.2 | 11q12.1 | ch-TOG | CTNND1 | |
| loss | 11q13.2 | 11q13.4 | LOC338692 | SKD3 | BCL1 at 11q13.3 (anti-apoptotic, amplified in breast cancer) // CCND1 at 11q13.3 (amplified in breast cancer [64]) // FGF3 at 11q13 |
| gain | 11q14.1 | 11q21 | Hs.26339.0 | MTMR2 | |
| loss | 11q23.3 | 11q23.3 | AMICA | HYOU1 | frequent loss of 11q23.3-q25 in neuroblastoma [65] // loss of 11q23 in 33% of 73 tumor types [66] |
| loss | 12p13.31 | 12p13.2 | TPI1 | CLEC1 | CDKN1B (alias p27Kip1) at 12p13.2 |
| loss | 12p12.3 | 12q12 | CGI-26 | MADP-1 | familial breast cancer at 12p12.1 (OMIM 114480) |
| gain | 12q14.2 | 12q22 | Hs.132260.0 | Hs.403150 | MDM2 at 12q15 // validated up-regulation of GPR49 at 12q21.1 |
| gain | 12q22 | 12q23.3 | USP44 | KIAA1033 | |
| loss | 12q23.3 | 12q24.11 | SART3 | Hs.18370.0 | loss of 12q24 in pancreas tumors [55] |
| gain | 13q14.11 | 13q22.1 | LOC283508 | PIBF1 | RB1 at 13q14.2 // ARLT1 at 13q14 // gain of expression and genomic amplification of 13q [17] |
| gain | 14q22.1 | 14q22.2 | PSMC6 | AND-1 | 14q22-q23 losses in 25% of tumor types [66] |
| loss | 14q24.1 | 14q24.3 | Hs.369329 | Hs.169812 | hereditary CRC at 14q24.3 (OMIM 114500) // loss of 14q24-31 in CRC metastases [36] // FOS at 14q24.3 // hereditary HNPCC7 at 14q24.3 (gene MLH3) (OMIM) // poor prognosis when 14q24-q31 is lost in renal cell carcinoma [67] // loss of expression and genomic DNA of 14q [17] |
| loss | 14q32.33 | 14q32.33 | ZFYVE21 | Hs.248015.0 | 14q32 is a tumor suppressive region in esophagal cancer [68] // loss of expression and genomic DNA of 14q [17] |
| loss | 15q21.1 | 15q22.31 | FBN1 | CLPX | association between loss of 15q21.1-q22.2 and survival in hepatocellular carcinoma [69] // allelic imbalance at 15q21.1 in breast cancer metastases [70] // loss of expression and genomic DNA of 15q [17] |
| loss | 15q26.1 | 15q26.3 | GABARAPL3 | FLJ25222 | loss of expression and genomic DNA of 15q [17] |
| loss | 16p12.1 | 16p11.2 | GTF3C1 | PRSS8 | |
| loss | 16q12.1 | 16q13 | TRF4-2 | FLJ13154 | |
| gain | 16q22.1 | 16q22.2 | PSMB10 | KIAA0931 | CDH1 (E-Cadherin) at 16q22.1 |
| loss | 17p13.3 | 17p13.2 | RPA1 | DHX33 | loss of 17p13.2 in CRC [25] // DHX33 at 17p13.2 |
| loss | 17p13.1 | 17p11.2 | GAS7 | COPS3 | Near TP53 at 17p13.1 .// hereditary CRC at 17p11.2 (OMIM 114500) // hereditary CRC at 17p13.1 (OMIM 114500) // // familial breast cancer at 17p13 (OMIM 114480) // loss of 17p12 in CRC [25] // ELAC2 at 17p11.2 |
| gain | 17q21.33 | 17q23.2 | TOB1 | PPM1D | NME1 (NME23) at 17q21.33 // familial breast cancer at 17q22-q23 (OMIM 114480) // |
| loss | 18p11.21 | 18q12.1 | MGC24180 | DSC3 | loss of expression and genomic DNA of 18 [17] |
| loss | 18q21.1 | 18q23 | CGBP | MBP | DCC at 18q21.3 (OMIM 120470) // loss of 18q21.1 in CRC cell lines [25] // SMAD2 // SMAD4 mutations in CRC [71] // loss of expression and genomic DNA of 18 [17] |
| loss | 19p13.3 | 19p13.3 | DF | APCL | |
| gain | 19p13.2 | 19p13.12 | FLJ20244 | NOTCH3 | |
| gain | 19p13.11 | 19q13.12 | LOC114977 | TYROBP | NIFIE14 at 19q13.12 |
| loss | 19q13.2 | 19q13.32 | MGC20255 | TOMM40 | AKT2 (breast carcinoma at 19q13.2 // TGFB1 at 19q13.2 // proapototic Bax at 19q13.33 |
| gain | 20p11.21 | 20q11.21 | C1QR1 | BCL2L1 | |
| gain | 20q11.22 | 20q11.23 | RNPC2 | C20orf102 | SRC at 20q11.23 (overexpressed in breast carcinoma) // gain of expression and genomic DNA of 20q [17] |
| gain | 20q13.12 | 20q13.33 | SLC12A5 | ARFRP1 | gain of expression and genomic DNA of 20q [17] |
| gain | 21q22.12 | 21q22.3 | C21orf18 | TMPRSS2 | ETS2 at 21q22.2 |
| loss | 21q22.3 | 21q22.3 | PFKL | COL6A1 | COL18A1 (Endostatin) at 21q22.3 |
| loss | 22q11.21 | 22q12.1 | SDF2L1 | TPST2 | familial breast cancer at 22q12.1 (OMIM 114480) |
| loss | 22q13.31 | 22q13.33 | Hs.296370.0 | RABL2B | hereditary CRC at 22q13 (OMIM 114500) |
| gain | Xp22.13 | Xp22.11 | SCML1 | ARX | |
| gain | Xp11.22 | Xp11.1 | Hs.3383.1 | Hs.224455 | |
| gain | Xq24 | Xq26.3 | FLJ32122 | CXX1 |
These are condensed results of the ChARM analyses: overlapping regions with evidence for up- or down-regulation from various analyses of different cross-correlation window sizes have been fused into single regions. The original ChARM output including p values for each region and additional annotation can be found in Additional file 1. Hereditary colorectal cancer syndromes are indicated along with their OMIM ID. Gene symbols are official or provisional HUGO symbols if available, otherwise names of Unigene clusters. Information about known tumor genes in misregulated regions were extracted from the literature. Tumor-associated genes are located within expression islands or in near vicinity.