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S6 Table. Outlier Gene List Identified by COPA

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S6 Table. Outlier gene list identified by COPA Lung cancer Breast cancer Gene Outlier types Gene Outlier types 1. Kinase, Predicted 1. Kinase, Predicted EPHA5 ERBB2 membrane proteins membrane proteins 1. Kinase, Predicted 1. Kinase, Predicted EPHA8 MGC42105 membrane proteins membrane proteins 1. Kinase, Predicted 1. Kinase, Predicted GUCY2C ROS1 membrane proteins membrane proteins 1. Kinase, Predicted BRDT 2. Kinase VRK2 membrane proteins CAMKV 2. Kinase BRDT 2. Kinase CDK4 2. Kinase CAMKV 2. Kinase CDKL4 2. Kinase CDK12 2. Kinase GRK1 2. Kinase CDK4 2. Kinase MAPK9 2. Kinase MOS 2. Kinase MOS 2. Kinase PAK1 2. Kinase MYT1 2. Kinase PDK3 2. Kinase 3. Predicted membrane ABCC12 PRKCG 2. Kinase proteins 3. Predicted membrane ABCC2 RIOK1 2. Kinase proteins 3. Predicted membrane ABCG5 RPS6KB1 2. Kinase proteins 3. Predicted membrane ACCN1 STK38L 2. Kinase proteins 3. Predicted membrane ADAM7 TLK2 2. Kinase proteins 3. Predicted membrane ADCY10 YSK4 2. Kinase proteins 3. Predicted membrane 3. Predicted membrane AGL ABCA13 proteins proteins 3. Predicted membrane 3. Predicted membrane ALG9 ACCN1 proteins proteins 3. Predicted membrane 3. Predicted membrane ASB5 ADRA1D proteins proteins 3. Predicted membrane 3. Predicted membrane ASGR2 AGPAT6 proteins proteins 3. Predicted membrane 3. Predicted membrane BEST3 ALG8 proteins proteins 3. Predicted membrane 3. Predicted membrane BSND ANO7 proteins proteins 3. Predicted membrane 3. Predicted membrane BTNL8 ART4 proteins proteins 3. Predicted membrane 3. Predicted membrane C14orf68 ATP2B3 proteins proteins 3. Predicted membrane 3. Predicted membrane C19orf28 BSND proteins proteins 3. Predicted membrane 3. Predicted membrane C20orf123 BTNL8 proteins proteins 3. Predicted membrane 3. Predicted membrane CA14 C17orf71 proteins proteins 3. Predicted membrane 3. Predicted membrane CABP7 C2orf82 proteins proteins 3. Predicted membrane 3. Predicted membrane CACNA1A C2orf85 proteins proteins 3. Predicted membrane 3. Predicted membrane CACNA1B C5orf60 proteins proteins 3. Predicted membrane 3. Predicted membrane CALY CABP7 proteins proteins 3. Predicted membrane 3. Predicted membrane CCKBR CALHM1 proteins proteins 3. Predicted membrane 3. Predicted membrane CDH12 CALHM3 proteins proteins 3. Predicted membrane 3. Predicted membrane CDH16 CCDC155 proteins proteins 3. Predicted membrane 3. Predicted membrane CDHR2 CCKAR proteins proteins 3. Predicted membrane 3. Predicted membrane CDHR5 CCKBR proteins proteins 3. Predicted membrane 3. Predicted membrane CHRNA9 CDH4 proteins proteins 3. Predicted membrane 3. Predicted membrane CHRNB2 CDH7 proteins proteins 3. Predicted membrane 3. Predicted membrane CLCA4 CDHR4 proteins proteins 3. Predicted membrane 3. Predicted membrane CLDN17 CDHR5 proteins proteins 3. Predicted membrane 3. Predicted membrane CLDN22 CDKAL1 proteins proteins 3. Predicted membrane 3. Predicted membrane CLEC2L CHRNA9 proteins proteins 3. Predicted membrane 3. Predicted membrane CLRN3 CLDN10 proteins proteins 3. Predicted membrane 3. Predicted membrane CNGB3 CLDN22 proteins proteins 3. Predicted membrane 3. Predicted membrane COL25A1 CLEC2L proteins proteins 3. Predicted membrane 3. Predicted membrane COX7A2L CLEC6A proteins proteins 3. Predicted membrane 3. Predicted membrane CREB3L3 CNTN6 proteins proteins 3. Predicted membrane 3. Predicted membrane CRHR1 COX11 proteins proteins 3. Predicted membrane 3. Predicted membrane CRHR2 CXorf59 proteins proteins 3. Predicted membrane 3. Predicted membrane CSMD3 CYP4A22 proteins proteins 3. Predicted membrane 3. Predicted membrane CTCFL ERGIC3 proteins proteins 3. Predicted membrane 3. Predicted membrane CUZD1 FATE1 proteins proteins 3. Predicted membrane 3. Predicted membrane CYP3A4 FBXO18 proteins proteins 3. Predicted membrane 3. Predicted membrane CYP4F8 FER1L6 proteins proteins 3. Predicted membrane 3. Predicted membrane DSC1 FUT5 proteins proteins 3. Predicted membrane 3. Predicted membrane DSG3 GABBR2 proteins proteins 3. Predicted membrane 3. Predicted membrane FADS6 GABRA5 proteins proteins 3. Predicted membrane 3. Predicted membrane FAM163A GABRQ proteins proteins 3. Predicted membrane 3. Predicted membrane FAM75A6 GALNT9 proteins proteins 3. Predicted membrane 3. Predicted membrane FER1L6 GCNT3 proteins proteins 3. Predicted membrane 3. Predicted membrane FURIN GDAP1L1 proteins proteins 3. Predicted membrane 3. Predicted membrane FXYD2 GDPD2 proteins proteins 3. Predicted membrane 3. Predicted membrane GABRA3 GDPD4 proteins proteins 3. Predicted membrane 3. Predicted membrane GABRR1 GFRA3 proteins proteins 3. Predicted membrane 3. Predicted membrane GABRR3 GJB6 proteins proteins 3. Predicted membrane 3. Predicted membrane GALNT8 GPR142 proteins proteins 3. Predicted membrane 3. Predicted membrane GALNTL5 GPR150 proteins proteins 3. Predicted membrane 3. Predicted membrane GALR2 GPR22 proteins proteins 3. Predicted membrane 3. Predicted membrane GCGR GPR25 proteins proteins 3. Predicted membrane 3. Predicted membrane GDPD2 GPR26 proteins proteins 3. Predicted membrane 3. Predicted membrane GJA10 GPR88 proteins proteins 3. Predicted membrane 3. Predicted membrane GJA3 GRIA1 proteins proteins 3. Predicted membrane 3. Predicted membrane GPR12 GRIN2C proteins proteins 3. Predicted membrane 3. Predicted membrane GPR139 GRIN3B proteins proteins 3. Predicted membrane 3. Predicted membrane GPR144 GSG1L proteins proteins 3. Predicted membrane 3. Predicted membrane GPR78 HAVCR1 proteins proteins 3. Predicted membrane 3. Predicted membrane GRIA4 HEPHL1 proteins proteins 3. Predicted membrane 3. Predicted membrane GRIK1 HRH3 proteins proteins 3. Predicted membrane 3. Predicted membrane GRIK5 HRK proteins proteins 3. Predicted membrane 3. Predicted membrane GRIN2C HTR3A proteins proteins 3. Predicted membrane 3. Predicted membrane GRPR HTR6 proteins proteins 3. Predicted membrane 3. Predicted membrane HEPACAM2 IL19 proteins proteins 3. Predicted membrane 3. Predicted membrane HEPHL1 IL20RB proteins proteins 3. Predicted membrane 3. Predicted membrane HFE2 KCNH6 proteins proteins 3. Predicted membrane 3. Predicted membrane HHATL KCNH7 proteins proteins 3. Predicted membrane 3. Predicted membrane HOXC11 KCNJ1 proteins proteins 3. Predicted membrane 3. Predicted membrane IGDCC3 KCNJ6 proteins proteins 3. Predicted membrane 3. Predicted membrane IMP5 KCNJ9 proteins proteins 3. Predicted membrane 3. Predicted membrane IQCF5 KCNK10 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNB2 KCNK9 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNC1 KIAA1409 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNH6 KIR2DL1 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNH7 KIRREL2 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNK10 KIRREL3 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNK18 LASS3 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNK9 LCT proteins proteins 3. Predicted membrane 3. Predicted membrane KCNN1 LCTL proteins proteins 3. Predicted membrane 3. Predicted membrane KCNQ2 LEMD1 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNT1 LHFPL4 proteins proteins 3. Predicted membrane 3. Predicted membrane KCNV1 LMAN1L proteins proteins 3. Predicted membrane 3. Predicted membrane KIAA1409 LOC100130933 proteins proteins 3. Predicted membrane 3. Predicted membrane KIR2DL1 LRRN4 proteins proteins 3. Predicted membrane 3. Predicted membrane KIRREL3 LYPD5 proteins proteins 3. Predicted membrane 3. Predicted membrane LASS3 MADCAM1 proteins proteins 3. Predicted membrane 3. Predicted membrane LEMD3 MC4R proteins proteins 3. Predicted membrane 3. Predicted membrane LHCGR MED24 proteins proteins 3. Predicted membrane 3. Predicted membrane LINGO2 MEGF11 proteins proteins 3. Predicted membrane 3. Predicted membrane LOC153328 MLC1 proteins proteins 3. Predicted membrane 3. Predicted membrane LOC388946 MS4A5 proteins proteins 3. Predicted membrane 3. Predicted membrane LPCAT4 MSLN proteins proteins 3. Predicted membrane 3. Predicted membrane LRRC66 MSLNL proteins proteins 3. Predicted membrane 3. Predicted membrane LYZL2 MUC13 proteins proteins 3. Predicted membrane 3. Predicted membrane MC5R MUC4 proteins proteins 3. Predicted membrane 3. Predicted membrane MDM1 NCR1 proteins proteins 3. Predicted membrane 3. Predicted membrane MFF NDUFA4L2 proteins proteins 3. Predicted membrane 3. Predicted membrane MRGPRE NDUFC2 proteins proteins 3. Predicted membrane 3. Predicted membrane MRGPRX1 NMBR proteins proteins 3. Predicted membrane 3. Predicted membrane MS4A13 NMUR2 proteins proteins 3. Predicted membrane 3. Predicted membrane MS4A5 NPHS1 proteins proteins 3. Predicted membrane 3. Predicted membrane NKAIN2 NTSR1 proteins proteins 3. Predicted membrane 3. Predicted membrane NNAT NUP107 proteins proteins 3. Predicted membrane 3. Predicted membrane NPBWR1 NUP210L proteins proteins 3. Predicted membrane 3. Predicted membrane NPBWR2 OCA2 proteins proteins 3. Predicted membrane 3. Predicted membrane NPFFR2 OPRK1 proteins proteins 3. Predicted membrane 3. Predicted membrane NPSR1 OR10AG1 proteins proteins 3. Predicted membrane 3. Predicted membrane NPY5R OR10C1 proteins proteins 3. Predicted membrane 3. Predicted membrane NRXN1 OR10J1 proteins proteins 3. Predicted membrane 3. Predicted membrane NTSR1 OR10T2 proteins proteins 3. Predicted membrane 3. Predicted membrane OR10A4 OR10X1 proteins proteins 3. Predicted membrane 3. Predicted membrane OR10A5 OR11H1 proteins proteins 3. Predicted membrane 3. Predicted membrane OR10G3 OR13C4 proteins proteins
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  • Supplementary Figure S4

    Supplementary Figure S4

    18DCIS 18IDC Supplementary FigureS4 22DCIS 22IDC C D B A E (0.77) (0.78) 16DCIS 14DCIS 28DCIS 16IDC 28IDC (0.43) (0.49) 0 ADAMTS12 (p.E1469K) 14IDC ERBB2, LASP1,CDK12( CCNE1 ( NUTM2B SDHC,FCGR2B,PBX1,TPR( CD1D, B4GALT3, BCL9, FLG,NUP21OL,TPM3,TDRD10,RIT1,LMNA,PRCC,NTRK1 0 ADAMTS16 (p.E67K) (0.67) (0.89) (0.54) 0 ARHGEF38 (p.P179Hfs*29) 0 ATG9B (p.P823S) (0.68) (1.0) ARID5B, CCDC6 CCNE1, TSHZ3,CEP89 CREB3L2,TRIM24 BRAF, EGFR (7p11); 0 ABRACL (p.R35H) 0 CATSPER1 (p.P152H) 0 ADAMTS18 (p.Y799C) 19q12 0 CCDC88C (p.X1371_splice) (0) 0 ADRA1A (p.P327L) (10q22.3) 0 CCNF (p.D637N) −4 −2 −4 −2 0 AKAP4 (p.G454A) 0 CDYL (p.Y353Lfs*5) −4 −2 Log2 Ratio Log2 Ratio −4 −2 Log2 Ratio Log2 Ratio 0 2 4 0 2 4 0 ARID2 (p.R1068H) 0 COL27A1 (p.G646E) 0 2 4 0 2 4 2 EDRF1 (p.E521K) 0 ARPP21 (p.P791L) ) 0 DDX11 (p.E78K) 2 GPR101, p.A174V 0 ARPP21 (p.P791T) 0 DMGDH (p.W606C) 5 ANP32B, p.G237S 16IDC (Ploidy:2.01) 16DCIS (Ploidy:2.02) 14IDC (Ploidy:2.01) 14DCIS (Ploidy:2.9) -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 Log Ratio Log Ratio Log Ratio Log Ratio 12DCIS 0 ASPM (p.S222T) Log Ratio Log Ratio 0 FMN2 (p.G941A) 20 1 2 3 2 0 1 2 3 2 ERBB3 (p.D297Y) 2 0 1 2 3 20 1 2 3 0 ATRX (p.L1276I) 20 1 2 3 2 0 1 2 3 0 GALNT18 (p.F92L) 2 MAPK4, p.H147Y 0 GALNTL6 (p.E236K) 5 C11orf1, p.Y53C (10q21.2); 0 ATRX (p.R1401W) PIK3CA, p.H1047R 28IDC (Ploidy:2.0) 28DCIS (Ploidy:2.0) 22IDC (Ploidy:3.7) 22DCIS (Ploidy:4.1) 18IDC (Ploidy:3.9) 18DCIS (Ploidy:2.3) 17q12 0 HCFC1 (p.S2025C) 2 LCMT1 (p.S34A) 0 ATXN7L2 (p.X453_splice) SPEN, p.P677Lfs*13 CBFB 1 2 3 4 5 6 7 8 9 10 11
  • Transcription of Platelet-Derived Growth Factor Receptor a in Leydig Cells Involves Specificity Protein 1 and 3

    Transcription of Platelet-Derived Growth Factor Receptor a in Leydig Cells Involves Specificity Protein 1 and 3

    125 Transcription of platelet-derived growth factor receptor a in Leydig cells involves specificity protein 1 and 3 Francis Bergeron1, Edward T Bagu1 and Jacques J Tremblay1,2 1Reproduction, Perinatal and Child Health, CHUQ Research Centre, CHUL Room T1-49, 2705 Laurier Boulevard, Que´bec, Que´bec, Canada G1V 4G2 2Department of Obstetrics and Gynecology, Faculty of Medicine, Centre for Research in Biology of Reproduction, Universite´ Laval, Que´bec, Que´bec, Canada G1V 0A6 (Correspondence should be addressed to J J Tremblay; Email: [email protected]) Abstract Platelet-derived growth factor (PDGF) A is secreted by Sertoli cells and acts on Leydig precursor cells, which express the receptor PDGFRA, triggering their differentiation into steroidogenically active Leydig cells. There is, however, no information regarding the molecular mechanisms that govern Pdgfra expression in Leydig cells. In this study, we isolated and characterized a 2.2 kb fragment of the rat Pdgfra 50-flanking sequence in the TM3 Leydig cell line, which endogenously expresses Pdgfra. A series of 50 progressive deletions of the Pdgfra promoter was generated and transfected in TM3 cells. Using this approach, two regions (K183/K154 and K154/K105), each conferring 46% of Pdgfra promoter activity, were identified. To better define the regulatory elements, trinucleotide mutations spanning the K154/K105 region were introduced by site-directed mutagenesis in the context of the K2.2kb Pdgfra promoter. Mutations that altered the TCCGAGGGAAAC sequence at K138 bp significantly decreased Pdgfra promoter activity in TM3 cells. Several proteins from TM3 nuclear extracts were found to bind to this G(C/A) motif in electromobility shift assay.
  • 1,25 Dihydroxyvitamin D-Mediated Orchestration of Anticancer

    1,25 Dihydroxyvitamin D-Mediated Orchestration of Anticancer

    Kovalenko et al. BMC Genomics 2010, 11:26 http://www.biomedcentral.com/1471-2164/11/26 RESEARCH ARTICLE Open Access 1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1 Pavlo L Kovalenko1, Zhentao Zhang1, Min Cui1, Steve K Clinton2, James C Fleet1* Abstract Background: Prostate cancer is the second leading cause of cancer mortality among US men. Epidemiological evidence suggests that high vitamin D status protects men from prostate cancer and the active form of vitamin D, 1a,25 dihydroxyvitamin D3 (1,25(OH)2D) has anti-cancer effects in cultured prostate cells. Still, the molecular mechanisms and the gene targets for vitamin D-mediated prostate cancer prevention are unknown. Results: We examined the effect of 1,25(OH)2D (+/- 100 nM, 6, 24, 48 h) on the transcript profile of proliferating RWPE1 cells, an immortalized, non-tumorigenic prostate epithelial cell line that is growth arrested by 1,25(OH)2D (Affymetrix U133 Plus 2.0, n = 4/treatment per time and dose). Our analysis revealed many transcript level changes at a 5% false detection rate: 6 h, 1571 (61% up), 24 h, 1816 (60% up), 48 h, 3566 (38% up). 288 transcripts were regulated similarly at all time points (182 up, 80 down) and many of the promoters for these transcripts contained putative vitamin D response elements. Functional analysis by pathway or Gene Set Analysis revealed early suppression of WNT, Notch, NF-kB, and IGF1 signaling. Transcripts related to inflammation were suppressed at 6 h (e.g.