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. 2006 Oct 24;95(10):1439–1447. doi: 10.1038/sj.bjc.6603433

Table 2. Gene expression analysis at 1q and correlation with copy number gain.

Consensus segment Clone ID on the chip Hugo gene symbol Gene name Localisation (start–end) (bp) Cytoband P-value 1 P-value 2
G1 pdzk1 PDZK1 PDZ domain containing 1 143403500–143439848 1q21.1   0.015
G1 h2bfq HIST2H2BE Histone 2, H2be 146631105–146633327 1q21.2    
G1 cra MTMR11 Myotubularin-related protein 11 146675639–146683822 1q21.2 0.09 0.011
G1 vps45b VPS45A Vacuolar protein sorting 45A 146814958–146892599 1q21.2 0.025 0.027
G1 ca14 CA14 Carbonic anhydrase XIV 147005313–147012571 1q21.2   0.019
G1 ensa ENSA Endosulfine alpha 147370158–147377163 1q21.3 0.05 0.025
G1 anxa9 ANXA9 Annexin A9 147729649–147743202 1q21.3    
G1 af1q MLLT11 Myeloid/lymphoid or mixed-lineage leukaemia; translocated to, 11 147807778–147816066 1q21.3   0.045
G1 pip5k1a PIP5K1A Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha 147897780–147948713 1q21.3 0.09  
               
G2 mtx1 MTX1 Metaxin 1 151952587–151957144 1q22   0.051
G2 c1orf2 C1orf2 Chromosome 1 open reading frame 2 151994882–152003120 1q22 ND ND
G2 hspc003 MAPBPIP Mitogen-activated protein-binding protein-interacting protein 152802478–152806168 1q22 0.076  
G2   RAB25 RAB25, member RAS oncogene family 152808855–152818122 1q22   0.001
G2 cct3 CCT3 Chaperonin containing TCP1, subunit 3 (gamma) 153056634–153085846 1q22   0.0003
G2 croc4 C1orf61 Chromosome 1 open reading frame 61 153128056–153153185 1q22   0.075
               
G3 usf1 USF1 Upstream transcription factor 1 157781513–157787199 1q23.3 0.009 0.007
G3 aldh9 ALDH9A1 Aldehyde dehydrogenase 9 family, member A1 162327485–162364132 1q24.1 0.088 0.022
G3 mpzl1 MPZL1 Myelin protein zero-like 1 164387268–164453994 1q24.2 0.05 0.070
G3 tbx19 TBX19 T-box 19 164946309–164979694 1q24.2   0.027
               
G4 plu-1 JARID1B Jumonji, AT rich interactive domain 1B (RBP2-like) 199162987–199245053 1q32.1 0.097 0.095
G4 sox13 SOX13 SRY (sex determining region Y)-box 13 200442674–200457500 1q32.1    
G4 pctk3 PCTK3 PCTAIRE protein kinase 3 201857380–201862760 1q32.1 0.05 0.001
               
G5 spuf NENF Neuron-derived neurotrophic factor 209222493–209235935 1q32.3   0.023
G5 esrrg ESRRG Oestrogen-related receptor gamma 212723109–213309462 1q41    
               
G6 arf1 ARF1 ADP-ribosylation factor 1 224655969–224672451 1q42.13 0.098  
G6 rab4 RAB4A RAB4A, member RAS oncogene family 225806272–225839911 1q42.13   0.020
G6 disc1 DISC1 Disrupted in schizophrenia 1 228235748–228635487 1q42.2   0.001
G6 tarbp1 TARBP1 TAR (HIV) RNA-binding protein 1 230818923–230906713 1q42.2   0.0009
G6 tbce TBCE Tubulin-specific chaperone e 231749924–231831433 1q42.3    
G6 chs1 LYST Lysosomal trafficking regulator 232120934–232326807 1q42.3   0.010
               
G7 hnrpu HNRPU Heterogeneous nuclear ribonucleoprotein U 241218474–241229338 1q44 ND ND

ND=not done and refers to Q–RT–PCR measurements which could not be performed.

RNA expression profiles of 307 genes located at 1q were analysed in a total of 29 breast cancer cell lines and 26 primary tumours. Genes presented correspond to the 30 genes selected by DS. Significance threshold was DS>0.32 corresponding to <0.01 false positive. Expression levels were quantified by Q–RT–PCR for 28 out of 30 genes (primer design was unsuccessful for c1orf2 and HNRPU). Quantitative PCR primer sequences are presented in Supplementary Table S2. The recently reported candidate oncogene RAB25, which was not present on our array, was quantified as a positive control. Quantitative RT–PCR data were analysed for differential expression using two t-test approaches; t-test 1 (noted P-value 1) indicates correlation with copy number gain; t-test 2 (P-value 2) differential expression with normal breast. Two significance thresholds were used; strict P=<0.05, tolerant P=<0.1, P-values>0.1 were considered as nonsignificant and only values within the tolerance limit are indicated. Cell lines analysed were: BRCAMZ01, MDAMB175, CAL51, MDAMB435, SKBR7, ZR7530, BT474, MCF7Rich, HS578T, MDAMB436, SUM149, SUM185, BT20, HCC1187, HCC1428, HCC1937, HCC1954, HCC2218, MDAMB157, MDAMB361, MDAMB468, SKBR3, T47D, UACC812 and ZR751.