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Table I: Incubation of Primary Human Endothelial Cells with IFN-Γ Results in a Significant Increase in the Transcription of 215 Genes

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Table I: Incubation of primary human endothelial cells with IFN-γ results in a significant increase in the transcription of 215 genes Locus Fold ID Accession # Name Symbol Changeb p value 6373 AF002985 chemokine (C-X-C motif) ligand 11 CXCL11 298.28 5.66E-06 6373 AF030514 chemokine (C-X-C motif) ligand 11 CXCL11 229.77 2.59E-08 3627 NM_001565 chemokine (C-X-C motif) ligand 10 CXCL10 178.82 1.86E-08 3620 M34455 indoleamine-pyrrole 2,3 dioxygenase INDO 117.81 3.77E-06 4283 NM_002416 chemokine (C-X-C motif) ligand 9 CXCL9 78.17 8.36E-07 2633 AW014593 guanylate binding protein 1, interferon-inducible, 67kDa GBP1 52.15 1.07E-03 2633 NM_002053 guanylate binding protein 1, interferon-inducible, 67kDa GBP1 43.83 6.36E-04 2633 BC002666 guanylate binding protein 1, interferon-inducible, 67kDa GBP1 27.75 6.19E-04 115362 BG545653 Guanylate binding protein 5 GBP5 27.12 1.50E-05 NAc AI075407 NAc NAc 25.87 2.24E-03 94240 AA633203 epithelial stromal interaction 1 (breast) EPSTI1 23.43 2.87E-05 NAc AW392551 NAc NAc 22.64 3.81E-06 5920 NM_004585 retinoic acid receptor responder (tazarotene induced) 3 RARRES3 19.87 9.68E-07 2634 BF509371 guanylate binding protein 2, interferon-inducible GBP2 19.58 2.15E-03 10673 AF134715 tumor necrosis factor (ligand) superfamily, member 13b TNFSF13B 19.38 1.18E-06 6890 NM_000593 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) TAP1 18.23 9.80E-07 6355 AI984980 chemokine (C-C motif) ligand 8 CCL8 17.67 5.16E-07 10537 NM_006398 gamma-aminobutyric acid (GABA) B receptor, 1 GABBR1 16.74 1.44E-05 51365 NM_015900 phospholipase A1 member A PLA1A 15.62 1.24E-04 115362 BG271923 Guanylate binding protein 5 GBP5 15.60 1.22E-04 10964 NM_006820 interferon-induced protein 44-like IFI44L 15.36 1.73E-03 3437 NM_001549 interferon-induced protein with tetratricopeptide repeats 3 IFIT3 14.98 2.03E-04 54625 AA056548 poly (ADP-ribose) polymerase family, member 14 PARP14 14.29 1.66E-04 151636 AA577672 deltex 3-like (Drosophila) DTX3L 13.56 5.42E-03 NAc AW151360 NAc NAc 13.18 4.11E-04 51056 NM_015907 leucine aminopeptidase 3 LAP3 11.64 2.40E-03 6376 U84487 chemokine (C-X3-C motif) ligand 1 CX3CL1 11.22 4.14E-03 proteasome (prosome, macropain) subunit, beta type, 9 (large 5698 NM_002800 multifunctional peptidase 2) PSMB9 11.12 9.12E-04 6398 BF939675 secreted and transmembrane 1 SECTM1 10.64 2.88E-02 2643 NM_000161 GTP cyclohydrolase 1 (dopa-responsive dystonia) GCH1 10.56 1.02E-03 219285 BE966604 sterile alpha motif domain containing 9-like SAMD9L 10.20 6.84E-04 1462 BF218922 chondroitin sulfate proteoglycan 2 (versican) CSPG2 10.19 1.51E-05 8743 NM_003810 tumor necrosis factor (ligand) superfamily, member 10 TNFSF10 10.06 5.33E-03 2634 NM_004120 guanylate binding protein 2, interferon-inducible GBP2 10.05 1.39E-04 80833 NM_014349 apolipoprotein L, 3 APOL3 9.50 1.19E-03 116071 AW083820 basic leucine zipper transcription factor, ATF-like 2 BATF2 9.45 4.60E-04 Transcribed locus, strongly similar to XP_498081.1 PREDICTED: NAc AI694413 similar to Olfactory receptor 2I2 [Homo sapiens] NAc 9.25 1.10E-03 219285 BE669858 sterile alpha motif domain containing 9-like SAMD9L 9.17 7.46E-04 NAc W58601 Transcribed locus NAc 9.00 1.71E-05 3600 NM_000585 interleukin 15 IL15 8.83 2.97E-03 1193 AI768628 chloride intracellular channel 2 CLIC2 8.68 3.43E-03 115361 BG260886 guanylate binding protein 4 GBP4 8.66 7.64E-04 3659 NM_002198 interferon regulatory factor 1 IRF1 8.61 1.96E-04 Locus Fold ID Accession # Name Symbol Changeb p value NAc AI608902 NAc NAc 8.07 1.11E-04 2635 AL136680 guanylate binding protein 3 GBP3 8.02 6.20E-03 3431 NM_004509 SP110 nuclear body protein SP110 8.01 2.52E-04 57674 AA233374 chromosome 17 open reading frame 27 C17orf27 7.75 1.19E-04 441168 AV734646 hypothetical protein LOC441168 RP1-93H18.5 7.66 3.68E-05 168537 AA858297 GTPase, IMAP family member 7 GIMAP7 7.59 1.64E-02 129607 AI742057 hypothetical protein LOC129607 LOC129607 7.51 8.40E-04 54739 AA142842 XIAP associated factor-1 BIRC4BP 7.46 2.97E-03 10068 AI521549 interleukin 18 binding protein IL18BP 7.39 3.52E-03 8743 AW474434 tumor necrosis factor (ligand) superfamily, member 10 TNFSF10 7.26 4.70E-02 64135 NM_022168 interferon induced with helicase C domain 1 IFIH1 7.06 6.11E-03 6891 AA573502 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) TAP2 6.92 5.58E-03 1462 NM_004385 chondroitin sulfate proteoglycan 2 (versican) CSPG2 6.75 4.71E-04 6648 R34841 Superoxide dismutase 2, mitochondrial SOD2 6.74 2.75E-02 140711 BF437747 Chromosome 20 open reading frame 118 C20orf118 6.47 2.37E-04 5359 AI825926 phospholipid scramblase 1 PLSCR1 6.47 7.01E-03 10346 AA083478 tripartite motif-containing 22 TRIM22 6.38 2.78E-02 3431 AF280094 SP110 nuclear body protein SP110 6.37 1.26E-03 140711 AA603344 Chromosome 20 open reading frame 118 C20orf118 6.32 5.77E-04 80830 NM_030641 apolipoprotein L, 6 APOL6 6.25 4.45E-05 3433 AA131041 interferon-induced protein with tetratricopeptide repeats 2 IFIT2 6.19 9.80E-03 23586 NM_014314 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58 6.18 3.26E-04 7412 NM_001078 vascular cell adhesion molecule 1 VCAM1 6.16 3.06E-03 28984 NM_014059 response gene to complement 32 RGC32 6.05 4.17E-04 2920 M57731 chemokine (C-X-C motif) ligand 2 CXCL2 6.01 3.42E-03 6773 H98105 signal transducer and activator of transcription 2, 113kDa STAT2 6.00 2.08E-04 9111 NM_004688 N-myc (and STAT) interactor NMI 5.98 4.20E-03 54625 AW297731 Poly (ADP-ribose) polymerase family, member 14 PARP14 5.98 4.68E-02 6772 BC002704 signal transducer and activator of transcription 1, 91kDa STAT1 5.89 3.99E-03 84166 AA005023 nucleotide-binding oligomerization domains 27 NOD27 5.71 8.38E-05 6376 NM_002996 chemokine (C-X3-C motif) ligand 1 CX3CL1 5.57 3.66E-03 83666 AF307338 poly (ADP-ribose) polymerase family, member 9 PARP9 5.56 7.29E-03 8519 AA749101 interferon induced transmembrane protein 1 (9-27) IFITM1 5.56 4.64E-03 8542 AF323540 apolipoprotein L, 1 APOL1 5.49 1.57E-05 219285 AI064690 Sterile alpha motif domain containing 9-like SAMD9L 5.44 1.58E-04 23780 BC004395 apolipoprotein L, 2 APOL2 5.40 3.00E-04 716 M18767 complement component 1, s subcomponent C1S 5.37 1.53E-02 145741 BE218239 Nuclear localized factor 1 NLF1 5.36 3.54E-03 7453 M61715 tryptophanyl-tRNA synthetase WARS 5.36 5.40E-03 NAc AI655467 Full length insert cDNA clone YX74D05 NAc 5.21 1.68E-03 55601 NM_017631 hypothetical protein FLJ20035 FLJ20035 5.19 7.30E-03 5359 NM_021105 phospholipid scramblase 1 PLSCR1 5.14 4.34E-02 7453 NM_004184 tryptophanyl-tRNA synthetase WARS 5.05 4.20E-05 9246 NM_004223 ubiquitin-conjugating enzyme E2L 6 UBE2L6 4.89 1.08E-04 3628 NM_002194 inositol polyphosphate-1-phosphatase INPP1 4.85 4.56E-03 myxovirus (influenza virus) resistance 1, interferon-inducible 4599 NM_002462 protein p78 (mouse) MX1 4.79 2.84E-03 Locus Fold ID Accession # Name Symbol Changeb p value AFFX- HUMISGF3A/ 6772 M97935_3 signal transducer and activator of transcription 1, 91kDa STAT1 4.79 1.86E-02 3428 BG256677 interferon, gamma-inducible protein 16 IFI16 4.78 4.76E-02 94240 BE645480 Epithelial stromal interaction 1 (breast) EPSTI1 4.73 3.07E-03 91543 AI337069 radical S-adenosyl methionine domain containing 2 RSAD2 4.67 1.58E-03 similar to Caspase-4 precursor (CASP-4) (ICH-2 protease) (TX 648470 AA041298 protease) (ICE(rel)-II) LOC648470 4.59 1.56E-02 NAc AA781795 NAc NAc 4.57 5.06E-04 v-maf musculoaponeurotic fibrosarcoma oncogene homolog 4094 AF055376 (avian) MAF 4.56 4.74E-04 11217 BG540494 A kinase (PRKA) anchor protein 2 AKAP2 4.33 1.57E-02 NAc AW964431 NAc NAc 4.32 4.06E-04 91543 AW189843 radical S-adenosyl methionine domain containing 2 RSAD2 4.19 1.15E-03 9021 AI244908 suppressor of cytokine signaling 3 SOCS3 4.17 1.90E-02 8767 AF064824 receptor-interacting serine-threonine kinase 2 RIPK2 4.17 1.51E-03 3660 NM_002199 interferon regulatory factor 2 IRF2 4.15 3.13E-02 CD74 molecule, major histocompatibility complex, class II 972 K01144 invariant chain CD74 4.13 8.22E-04 3430 BC001356 interferon-induced protein 35 IFI35 4.08 4.83E-03 4939 NM_016817 2'-5'-oligoadenylate synthetase 2, 69/71kDa OAS2 4.07 3.39E-02 25939 AF147427 SAM domain and HD domain 1 SAMHD1 4.06 8.93E-03 7444 NM_006296 vaccinia related kinase 2 VRK2 4.04 8.94E-03 55859 NM_018476 brain expressed, X-linked 1 BEX1 3.99 1.78E-04 843 NM_001230 caspase 10, apoptosis-related cysteine peptidase CASP10 3.96 2.36E-04 3601 NM_002189 interleukin 15 receptor, alpha IL15RA 3.89 1.09E-03 64108 NM_022147 receptor transporter protein 4 RTP4 3.88 2.53E-04 1052 NM_005195 CCAAT/enhancer binding protein (C/EBP), delta CEBPD 3.85 4.59E-03 8519 NM_003641 interferon induced transmembrane protein 1 (9-27) IFITM1 3.82 2.15E-02 6737 NM_003141 tripartite motif-containing 21 TRIM21 3.82 2.09E-03 caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, 834 M87507 convertase) CASP1 3.78 1.87E-02 121506 AI051248 chromosome 12 open reading frame 46 C12orf46 3.77 1.23E-03 10384 NM_006994 butyrophilin, subfamily 3, member A3 BTN3A3 3.76 1.63E-02 6772 NM_007315 signal transducer and activator of transcription 1, 91kDa STAT1 3.73 4.25E-03 3431 AF280095 SP110 nuclear body protein SP110 3.68 1.46E-02 54739 NM_017523 XIAP associated factor-1 BIRC4BP 3.67 1.11E-03 4938 NM_016816 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 3.65 2.08E-02 55905 NM_018683 zinc finger protein 313 ZNF313 3.65 4.76E-03 10561 NM_006417 interferon-induced protein 44 IFI44 3.59 3.35E-02 961 BG230614 CD47 molecule CD47 3.58 1.88E-02 55281 NM_018295 transmembrane protein 140 TMEM140 3.55 2.69E-03 2355 N36408 FOS-like antigen 2 FOSL2 3.51 2.06E-02 55905 AF090934 zinc finger protein
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  • Long, Noncoding RNA Dysregulation in Glioblastoma

    Long, Noncoding RNA Dysregulation in Glioblastoma

    cancers Review Long, Noncoding RNA Dysregulation in Glioblastoma Patrick A. DeSouza 1,2 , Xuan Qu 1, Hao Chen 1,3, Bhuvic Patel 1 , Christopher A. Maher 2,4,5,6 and Albert H. Kim 1,6,* 1 Department of Neurological Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; [email protected] (P.A.D.); [email protected] (X.Q.); [email protected] (H.C.); [email protected] (B.P.) 2 Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; [email protected] 3 Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 4 Department of Biomedical Engineering, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 5 McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA 6 Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA * Correspondence: [email protected] Simple Summary: Developing effective therapies for glioblastoma (GBM), the most common primary brain cancer, remains challenging due to the heterogeneity within tumors and therapeutic resistance that drives recurrence. Noncoding RNAs are transcribed from a large proportion of the genome and remain largely unexplored in their contribution to the evolution of GBM tumors. Here, we will review the general mechanisms of long, noncoding RNAs and the current knowledge of how these impact heterogeneity and therapeutic resistance in GBM. A better understanding of the molecular drivers required for these aggressive tumors is necessary to improve the management and outcomes Citation: DeSouza, P.A.; Qu, X.; of this challenging disease.
  • Fine Mapping of the Hereditary Haemorrhagic Telangiectasia (HHT)3 Locus on Chromosome 5 Excludes VE-Cadherin-2, Sprouty4 And

    Fine Mapping of the Hereditary Haemorrhagic Telangiectasia (HHT)3 Locus on Chromosome 5 Excludes VE-Cadherin-2, Sprouty4 And

    Govani and Shovlin Journal of Angiogenesis Research 2010, 2:15 http://www.jangiogenesis.com/content/2/1/15 JOURNAL OF ANGIOGENESIS RESEARCH RESEARCH Open Access Fine mapping of the hereditary haemorrhagic telangiectasia (HHT)3 locus on chromosome 5 excludes VE-Cadherin-2, Sprouty4 and other interval genes Fatima S Govani, Claire L Shovlin* Abstract Background: There is significant interest in new loci for the inherited condition hereditary haemorrhagic telangiectasia (HHT) because the known disease genes encode proteins involved in vascular transforming growth factor (TGF)-b signalling pathways, and the disease phenotype appears to be unmasked or provoked by angiogenesis in man and animal models. In a previous study, we mapped a new locus for HHT (HHT3) to a 5.7 Mb region of chromosome 5. Some of the polymorphic markers used had been uninformative in key recombinant individuals, leaving two potentially excludable regions, one of which contained loci for attractive candidate genes encoding VE Cadherin-2, Sprouty4 and FGF1, proteins involved in angiogenesis. Methods: Extended analyses in the interval-defining pedigree were performed using informative genomic sequence variants identified during candidate gene sequencing. These variants were amplified by polymerase chain reaction; sequenced on an ABI 3730xl, and analysed using FinchTV V1.4.0 software. Results: Informative genomic sequence variants were used to construct haplotypes permitting more precise citing of recombination breakpoints. These reduced the uninformative centromeric region from 141.2-144 Mb to between 141.9-142.6 Mb, and the uninformative telomeric region from 145.2-146.9 Mb to between 146.1-146.4 Mb. Conclusions: The HHT3 interval on chromosome 5 was reduced to 4.5 Mb excluding 30% of the coding genes in the original HHT3 interval.