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Gene Expression Study of Mycobacterium Avium Subspecies

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Gene Expression Study of Mycobacterium Avium Subspecies University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2014-02-05 Gene Expression Study Of Mycobacterium avium subspecies paratuberculosis Infected Cows – “A road to identify transcripts that could serve as biomarkers for early diagnosis of Johne’s disease” David, Joel David, J. (2014). Gene Expression Study Of Mycobacterium avium subspecies paratuberculosis Infected Cows – “A road to identify transcripts that could serve as biomarkers for early diagnosis of Johne’s disease” (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/26265 http://hdl.handle.net/11023/1368 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca List of upstream regulators and their targets in differentially expressed genes at 9 months after infection © 2000-2013 Ingenuity Systems, Inc. All rights reserved. Upstream Regulator Fold Change Molecule Type Predicted Activation State Activation z-score p-value of overlap Target molecules in dataset HIF1A transcription regulator Inhibited -2.200 2.11E-01 ACO1,ATP2A2,CCR7,FHL3,NTRK2,SLC29A1 miR-1972 (miRNAs w/seed CAGGCCA) mature microRNA Inhibited -2.200 2.65E-01 C3orf45,FPGS,MAT1A,PRDX1,ZBTB33 simvastatin chemical drug Inhibited -2.184 3.28E-02 ACVR1,ANXA3,BAX,CCL3,NTRK2,STAT4 prednisolone chemical drug Inhibited -2.121 9.93E-03 ATG4A,BAX,GABARAPL1,PRDX1,RPS6KB1,SNCA,TNFSF10,UTRN miR-516a-3p (and other miRNAs w/seed GCUUCCU) mature microRNA Inhibited -2.000 6.09E-02 BTBD7,STAT4,SVOP,TTC37 miR-2115-5p (miRNAs w/seed GCUUCCA) mature microRNA Inhibited -2.000 8.01E-02 BTBD7,CLPTM1L,GCFC2,RPS6KB1 miR-544b (miRNAs w/seed CCUGAGG) mature microRNA -1.987 1.67E-01 CMTM3,CMTM7,UNC93A,UQCRFS1 POU5F1 transcription regulator -1.982 9.98E-03 ASH2L,JARID2,PHC1,SH3GLB1,STIM1 topotecan chemical drug -1.982 1.02E-01 FUBP1,MAP2K5,OSBPL8,PLK3 miR-4530 (miRNAs w/seed CCAGCAG) mature microRNA -1.964 3.33E-01 CYB5B,ERLIN2,OGDHL,RSAD1 miR-1827 (and other miRNAs w/seed GAGGCAG) mature microRNA -1.951 1.00E00 COBLL1,CXADR,SPDEF,SYT9 prostaglandin E2 chemical - endogenous mammalian -1.944 2.96E-01 BAX,CCL3,CCR7,FST,MXI1 sirolimus chemical drug -1.937 2.55E-01 BAX,CCR7,IL4R,LDHB,RPL15,RPS12,RPS6KB1 camptothecin chemical toxicant -1.800 6.07E-03 APPBP2,ARHGEF1,BAX,CCL3,CD53,CXCR5,FES,HLA-A,MAP2K5,MNAT1,OPTN,PIK3CA,TBL1X,TNK2,WNK1,ZNF408 miR-132-3p (and other miRNAs w/seed AACAGUC) mature microRNA -1.783 1.65E-02 ACVR1,BTBD7,CLYBL,COLQ,JOSD1,NFAT5,NREP,OSBPL8,SETD5,UBN1,VDAC2,VTI1A miR-16-5p (and other miRNAs w/seed AGCAGCA) mature microRNA -1.309 3.03E-02 AHCYL2,ARL3,C2orf43,C9orf69,CDK5RAP1,CHD9,COBLL1,CRIM1,DHDDS,ERLIN2,FUBP1,GABARAPL1,GORASP2,HECTD4,JARID2,KHNYN,LEPREL1,MAP1A,MTMR3,OOEP,RAPGEF2,RHOBTB2,SLC38A1,SOS2,STIM1,TIA1,VTI1A,ZBTB33 tacrolimus chemical drug -1.195 4.27E-03 ARHGEF1,BATF,BAX,CDK13,CXADR,NFAT5,PA2G4,TNFSF10 miR-486-5p (and other miRNAs w/seed CCUGUAC) mature microRNA -1.188 3.13E-02 CXCR5,MXI1,NFAT5,NUDCD1,SLC38A1,TBL1X,VTI1A miR-3197 (miRNAs w/seed GAGGCGC) mature microRNA -1.131 4.06E-02 CMTM3,FPGS,SIN3B,TMEM79 CD3 complex -1.122 1.06E-02 BATF,CCL3,CD5,CD53,GOLGB1,IL4R,LEF1,MST1,NFAT5,PA2G4,PDIA4,S100A11,STIM1,TNFSF10,VDAC2,YY1 miR-4708-5p (miRNAs w/seed GAGAUGC) mature microRNA -1.119 1.04E-02 ANXA3,ATF1,CSF2RA,FST miR-4428 (miRNAs w/seed AAGGAGA) mature microRNA -1.067 7.40E-03 BCDIN3D,CELF1,SCRN3,TMLHE miR-374b-5p (and other miRNAs w/seed UAUAAUA) mature microRNA -1.052 1.96E-03 ADNP,BTBD7,CHD9,CRIM1,CXADR,DIP2C,FECH,HECTD4,HEG1,MED13,MEF2D,PMEPA1,PNRC1,RAB5B,SCRN3,SETD2,UBAP2L,ZDHHC5,ZMYM1 TP73 transcription regulator -0.998 3.21E-02 BAX,ERCC2,IL4R,PNRC1,TBL1X,TRIM32 miR-3162-3p (miRNAs w/seed CCCUACC) mature microRNA -0.911 2.57E-02 ACVR1,GABARAPL1,OPTN,PHC1,S1PR1,SDHC miR-124-3p (and other miRNAs w/seed AAGGCAC) mature microRNA -0.883 4.21E-02 ARHGEF1,BTBD7,CDK13,CXADR,DDX6,DHDDS,FPGS,GPR173,LUC7L2,NFAT5,OSBPL8,PCSK6,PER3,PIK3CA,PMEPA1,PXMP4,RAB34,RAPGEF2,RPS6KB1,SART3,SH3GLB1,SLC29A1,SOS2,SSH1,TEX261,TIA1,TMLHE,TPCN1,TRABD,UBN1,WDR81,WNK1 miR-214-3p (and other miRNAs w/seed CAGCAGG) mature microRNA -0.883 2.34E-02 ATP2A2,BCDIN3D,CELF1,COLQ,ERLIN2,MICU1,MTMR3,NSD1,PPIP5K1,RAB34,RAB5B,RHOBTB2,RSAD1,SNCA,TNK2,UBAP2L,USP20,VTI1A miR-1321 (and other miRNAs w/seed AGGGAGG) mature microRNA -0.848 4.36E-02 AHCY,AHCYL2,HECTD4,MEF2D,MTMR3,NFAT5,SSH1,STIM1 XBP1 transcription regulator -0.816 1.50E-02 ATF6B,ATP2A2,Gkn3,GOLGB1,GORASP2,PDIA4,S1PR1 IL4 cytokine -0.806 4.76E-02 BAX,CCL3,CCR7,CD5,CXCR5,DGKA,EPHX1,IL4R,LEF1,PSMB8,PTPRCAP,SLC29A1,SMG7,STAT4,VTI1A miR-24-3p (and other miRNAs w/seed GGCUCAG) mature microRNA -0.781 2.36E-03 AGPAT1,ATG4A,CMTM3,CXADR,FST,GPR173,HEG1,MBD6,MEN1,MTMR3,MXI1,NFAT5,NREP,PHC1,PLK3,PMEPA1,PXMP4,RAB5B,S1PR1,VTI1A miR-3679-3p (miRNAs w/seed UUCCCCC) mature microRNA -0.722 2.42E-03 AUTS2,CHD9,DDX6,FST,FUBP1,GABARAPL1,PEBP1,PPP4R1,PRRC2A,SPDEF,SSTR2,TBL1X,TMLHE,TNFSF10,VTI1A miR-4652-5p (miRNAs w/seed GGGGACU) mature microRNA -0.670 1.57E-02 ATF6B,LPPR2,NSD1,PXMP4,RHOBTB2,SLC38A1,TIA1,VTI1A miR-155-5p (miRNAs w/seed UAAUGCU) mature microRNA -0.627 4.27E-02 C9orf69,CCL3,CHD9,FUBP1,JARID2,NFAT5,RAB34,S1PR1,TIA1,TRIM32,VTI1A,WNK1,YWHAE miR-4763-5p (miRNAs w/seed GCCUGCC) mature microRNA -0.608 1.29E-02 CXCR5,DHDDS,LPPR2,MICU1,NDUFA11,PCSK6,PLEKHG2,PRDX1,PXMP4,SIN3B,SSH1,SVOP,SYT9,TEX261 miR-495-3p (and other miRNAs w/seed AACAAAC) mature microRNA -0.579 2.04E-02 APPBP2,CELF1,CNR1,CRIM1,CYB5B,FUBP1,JOSD1,MPRIP,NFAT5,PLEKHG2,PNRC1,PRRC2A,SDHC,SLC25A26,SNCA,TEX261,UBN1,VDAC2,VPS13D,WNK1 miR-4308 (and other miRNAs w/seed CCCUGGA) mature microRNA -0.564 1.04E-02 AHCYL2,APPBP2,CELF1,NRBP2,PDIA4,PPIP5K1,SH3GLB1,SVOP,WDR81 IFN alpha/beta group -0.555 2.20E-02 BAX,CCR7,HLA-A,TNFSF10 miR-1225-3p (miRNAs w/seed GAGCCCC) mature microRNA -0.552 4.79E-02 APOBR,DDX6,GORASP2,MEF2D,SLC29A1,TEX261,UBN1,UNC93A,VTI1A miR-129-5p (miRNAs w/seed UUUUUGC) mature microRNA -0.529 1.52E-02 AUTS2,C9orf69,CELF1,MEF2D,MTMR3,PMEPA1,RHOBTB2,RPS6KB1,SNAPC3,SSH1,SSTR2,TBL1X,TNRC6C,ZBTB33 cyclosporin A biologic drug -0.529 2.67E-04 ARHGEF1,BATF,BAX,CCR7,CDK13,DGKA,FST,GSTM3,NFAT5,PA2G4,PSMB8,S100A11,TNFSF10,UTRN,VDAC2 miR-181a-5p (and other miRNAs w/seed ACAUUCA) mature microRNA -0.477 3.36E-02 AP1AR,ARL3,ATP2A2,CHD9,CNOT1,CNR1,CRIM1,CXADR,DIP2C,ERLIN2,JARID2,MAP1A,NFAT5,OSBPL8,PER3,RAPGEF2,RPS6KB1,S1PR1,SH3GLB1,SIN3B,TBL1X,WNK1,YY1,ZBTB33 gentamicin chemical drug -0.469 4.98E-03 ATIC,BAX,CDK13,HSPB1,Nrg1,PDIA4,PSMB8,SART3,SLC9A3 lenalidomide chemical drug -0.447 2.83E-02 AUTS2,BTBD7,CCL3,NUDCD1,UTRN miR-133a-3p (and other miRNAs w/seed UUGGUCC) mature microRNA -0.421 1.43E-02 AP1AR,ARL3,ATP2A2,CDK13,CELF1,CNOT1,GABARAPL1,GPR173,NFAT5,PPIP5K1,RAB34,SMPD4,SNCA,SVOP,SYT9,TBL1X,TTYH3 miR-3691-5p (miRNAs w/seed GUGGAUG) mature microRNA -0.339 2.03E-02 DNMBP,PLEKHG2,TIA1,ZNF274 BCL6 transcription regulator -0.339 2.51E-02 BAX,CCL3,CCR7,CXCR5,IL4R miR-27a-3p (and other miRNAs w/seed UCACAGU) mature microRNA -0.327 4.85E-02 ADD1,APPBP2,CNOT1,CNR1,COLQ,CXADR,GLT25D2,GPR173,HEG1,MED13,MFHAS1,MXI1,NFAT5,NGFRAP1,NREP,NSD1,PDIA5,PHF13,RAPGEF2,RPS6KB1,SFSWAP,SSH1,TIA1,WNK1 miR-149-5p (miRNAs w/seed CUGGCUC) mature microRNA -0.323 6.55E-03 ATP2A2,CD5,CMTM3,CYB5B,JOSD1,MTMR3,NFAT5,NSD1,NTRK2,OGDHL,PHC1,PPIP5K1,RHOBTB2,TBL1X,TEX261,TNK2 6-hydroxydopamine chemical toxicant -0.304 4.28E-03 ACO1,BAX,CNR1,MEF2D,SNCA miR-377-3p (miRNAs w/seed UCACACA) mature microRNA -0.254 2.99E-02 BTBD7,CELF1,CNR1,GPR173,MAP1A,MPRIP,MTMR3,NSD1,OGDHL,PDIA4,RPE,RPS6KB1,SETD5,STIM1,TBL1X miR-4323 (miRNAs w/seed AGCCCCA) mature microRNA -0.245 1.87E-02 AHCY,BCDIN3D,DHDDS,ME3,NRBP2,NSD1,SIN3B,STIM1 miR-873-5p (and other miRNAs w/seed CAGGAAC) mature microRNA -0.233 1.82E-03 AHCYL2,APPBP2,CRIM1,GOLGB1,LRRC41,PER3,PPP4R1,PXMP4,SDHC,SLC25A3,TIA1,WDR6,YWHAE miR-29b-3p (and other miRNAs w/seed AGCACCA) mature microRNA -0.232 4.76E-02 BTBD7,C16orf88,C9orf69,CNR1,DIP2C,ERLIN2,JARID2,JOSD1,MAT1A,NFAT5,NREP,NSD1,PER3,PHC1,SETD5,SH3GLB1,SYT9,USP34,WDR81,YWHAE,YY1,ZDHHC5 doxorubicin chemical drug -0.227 3.76E-02 ATP2A2,BAX,GSTM3,PMEPA1,PRDX1,PSMB8,S100A11,TNFSF10,UQCRFS1 miR-197-3p (and other miRNAs w/seed UCACCAC) mature microRNA -0.218 1.50E-02 ACVR1,CD53,CLYBL,DIP2C,ERLIN2,GOLGB1,RAB5B,SVOP,VTI1A EDN1 cytokine -0.182 3.06E-02 ATP2A2,CCR7,FST,MPRIP,Nrg1,YWHAE cisplatin chemical drug -0.172 2.49E-03 BAX,CD53,DGKA,GSTM3,IL4R,LDHB,MAT1A,MTMR3,NREP,PEBP1,PIK3CA,PLK3,PSMB8,RHOBTB2,S100A11,TNFSF10,TNK2 miR-3714 (miRNAs w/seed AAGGCAG) mature microRNA -0.132 4.87E-02 ADNP,CMTM7,PLEKHG2,TRIM32 miR-130a-3p (and other miRNAs w/seed AGUGCAA) mature microRNA -0.118 7.05E-03 ACVR1,BTBD7,C9orf69,CNR1,DDX6,DIP2C,ENPP5,HEG1,JARID2,PMEPA1,PNRC1,PXMP4,RAB34,RAB5B,S1PR1,SOS2,TEX261,TNRC6C,TTYH3,UBAP2L,VPS13D,WNK1 miR-590-3p (miRNAs w/seed AAUUUUA) mature microRNA -0.107 4.46E-02 ADD1,APPBP2,ARL3,AUTS2,C16orf88,CDK13,CHD9,CNR1,CYFIP1,ERLIN2,GOLGB1,HEG1,MED13,MMAA,NFAT5,OPTN,OSBPL8,PPP4R1,RPL15,SH3GLB1,TNRC6C,USP34,VTI1A,WNK1 miR-4687-5p (miRNAs w/seed AGCCCUC) mature microRNA -0.080 1.76E-02 MTMR3,PXMP4,SDHC,SYT9,WNK1 mono-(2-ethylhexyl)phthalate chemical toxicant 0.000 2.20E-02 ACO1,BAX,CASP8AP2,SDHC,TRIM41,UQCRFS1 STAT6 transcription regulator 0.074 6.29E-03 BAX,CCR7,DGKA,EPHX1,IL4R,S100A11,SPDEF,STAT4 miR-19b-3p (and other
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