Experts and Doctors on gene expression profiling in Vancouver, British Columbia, Canada

Summary

Locale: Vancouver, British Columbia, Canada
Topic: gene expression profiling

Top Publications

  1. Smith D, Park J, Tiedje J, Mohn W. A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism. J Bacteriol. 2007;189:6195-204 pubmed
    ..Also, 7-oxo-PaA was identified as a metabolite of both AbA and PaA. Sequence analysis indicates that genes encoding this pathway have been horizontally transferred among Betaproteobacteria and Gammaproteobacteria. ..
  2. Chari R, Coe B, Wedseltoft C, Benetti M, Wilson I, Vucic E, et al. SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. BMC Bioinformatics. 2008;9:422 pubmed publisher
  3. Gomez P, Hackett T, Moore M, Knight D, Tebbutt S. Functional genomics of human bronchial epithelial cells directly interacting with conidia of Aspergillus fumigatus. BMC Genomics. 2010;11:358 pubmed publisher
    ..fumigatus with human cells derived from individuals with or without underlying disease susceptibility. ..
  4. Wu C, Wyatt A, Lapuk A, McPherson A, McConeghy B, Bell R, et al. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol. 2012;227:53-61 pubmed publisher
    ..Overall, this work highlights the importance of integrated analyses of genome, exome and transcriptome sequences for basic tumour biology, sequence-based molecular pathology and personalized oncology. ..
  5. Wei W, Hou J, Alder O, Ye X, Lee S, Cullum R, et al. Genome-wide microRNA and messenger RNA profiling in rodent liver development implicates mir302b and mir20a in repressing transforming growth factor-beta signaling. Hepatology. 2013;57:2491-501 pubmed publisher
    ..Collectively, we uncovered dynamic patterns of individual miRNAs during liver development, as well as miRNA networks that could be essential for the specification and differentiation of liver progenitors. (HEPATOLOGY 2013). ..
  6. Buschdorf J, Ong M, Ong S, Macisaac J, Chng K, Kobor M, et al. Low birth weight associates with hippocampal gene expression. Neuroscience. 2016;318:190-205 pubmed publisher
    ..The data also provide a potential molecular basis for the developmental origin of an enhanced risk for mental disorders. ..
  7. Yang G, Banks K, Bonaguro R, Wilson G, Dreolini L, de Leeuw C, et al. Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the Hprt1 locus. Genomics. 2009;93:196-204 pubmed publisher
    ..We have validated our tools as part of the Pleiades Promoter Project (http://www.pleiades.org), with the generation of brain-specific EGFP positive germline mouse strains. ..
  8. Gascoyne R, Rosenwald A, Poppema S, Lenz G. Prognostic biomarkers in malignant lymphomas. Leuk Lymphoma. 2010;51 Suppl 1:11-9 pubmed publisher
    ..This review focuses on recent advances in translational and clinical research on biomarkers in malignant lymphomas. ..
  9. Jardon M, Sattha B, Braasch K, Leung A, Cote H, Butler M, et al. Inhibition of glutamine-dependent autophagy increases t-PA production in CHO cell fed-batch processes. Biotechnol Bioeng. 2012;109:1228-38 pubmed publisher
    ..Monitoring or genetic engineering of autophagy provides novel avenues to improve the performance of cell culture-based recombinant protein production. ..

More Information

Publications193 found, 100 shown here

  1. Guggisberg A, Lai Z, Huang J, Rieseberg L. Transcriptome divergence between introduced and native populations of Canada thistle, Cirsium arvense. New Phytol. 2013;199:595-608 pubmed publisher
    ..The fact that genotypes from the Midwest exhibit different expression kinetics than remaining North American samples further corroborates the hypothesis that the New World has been colonized twice, independently. ..
  2. Goytain A, Hines R, Quamme G. Huntingtin-interacting proteins, HIP14 and HIP14L, mediate dual functions, palmitoyl acyltransferase and Mg2+ transport. J Biol Chem. 2008;283:33365-74 pubmed publisher
    ..We conclude that the huntingtin interacting protein genes, HIP14 and HIP14L, encode Mg2+ transport proteins that are regulated by their innate palmitoyl acyltransferases thus fulfilling the characteristics of "chanzymes." ..
  3. Wang G, Wang J, Sadar M. Crosstalk between the androgen receptor and beta-catenin in castrate-resistant prostate cancer. Cancer Res. 2008;68:9918-27 pubmed publisher
    ..These studies provide the first in vivo evidence to support aberrant activation of the AR through the Wnt/beta-catenin signaling pathway during progression of prostate cancer to the terminal castrate-resistant stage...
  4. Cheang M, Chia S, Voduc D, Gao D, Leung S, Snider J, et al. Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst. 2009;101:736-50 pubmed publisher
    ..Expression of ER, progesterone receptor, and HER2 proteins and the Ki67 index appear to distinguish luminal A from luminal B breast cancer subtypes. ..
  5. Morozova O, Hirst M, Marra M. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet. 2009;10:135-51 pubmed publisher
  6. Pradhan M, Risberg B, Trope C, van de Rijn M, Gilks C, Lee C. Gross genomic alterations and gene expression profiles of high- grade serous carcinoma of the ovary with and without BRCA1 inactivation. BMC Cancer. 2010;10:493 pubmed publisher
  7. Keeling C, Weisshaar S, Ralph S, Jancsik S, Hamberger B, Dullat H, et al. Transcriptome mining, functional characterization, and phylogeny of a large terpene synthase gene family in spruce (Picea spp.). BMC Plant Biol. 2011;11:43 pubmed publisher
    ..These compounds contribute to defence against herbivores and pathogens and perhaps also protect against abiotic stress...
  8. Zhang P, Wang D, Zhao Y, Ren S, Gao K, Ye Z, et al. Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT-mTORC1 activation. Nat Med. 2017;23:1055-1062 pubmed publisher
  9. Selva D, Hammond G. Human sex hormone-binding globulin is expressed in testicular germ cells and not in sertoli cells. Horm Metab Res. 2006;38:230-5 pubmed
    ..These remarkable differences in human SHBG expression in the testis, when compared to other mammals, force us to reconsider the functional significance of SHBG expression in the testis in relation to male reproduction. ..
  10. Wang G, Jones S, Marra M, Sadar M. Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells. Oncogene. 2006;25:7311-23 pubmed
  11. Cohen Freue G, Holzer T, Forney J, McMaster W. Global gene expression in Leishmania. Int J Parasitol. 2007;37:1077-86 pubmed
  12. Cosseau C, Devine D, Dullaghan E, Gardy J, Chikatamarla A, Gellatly S, et al. The commensal Streptococcus salivarius K12 downregulates the innate immune responses of human epithelial cells and promotes host-microbe homeostasis. Infect Immun. 2008;76:4163-75 pubmed publisher
    ..S. salivarius K12 might thereby ensure that it is tolerated by the host and maintained on the epithelial surface while actively protecting the host from inflammation and apoptosis induced by pathogens. ..
  13. McPhee J, Tamber S, Bains M, Maier E, Gellatly S, Lo A, et al. The major outer membrane protein OprG of Pseudomonas aeruginosa contributes to cytotoxicity and forms an anaerobically regulated, cation-selective channel. FEMS Microbiol Lett. 2009;296:241-7 pubmed publisher
  14. Chari R, Lonergan K, Pikor L, Coe B, Zhu C, Chan T, et al. A sequence-based approach to identify reference genes for gene expression analysis. BMC Med Genomics. 2010;3:32 pubmed publisher
    ..Significantly, the approach used in this study can be applied to data generated using new generation sequencing platforms for the identification of reference genes optimal within diverse contexts. ..
  15. Philippe R, Ralph S, Mansfield S, Bohlmann J. Transcriptome profiles of hybrid poplar (Populus trichocarpa × deltoides) reveal rapid changes in undamaged, systemic sink leaves after simulated feeding by forest tent caterpillar (Malacosoma disstria). New Phytol. 2010;188:787-802 pubmed publisher
    ..Systemic transcriptome changes of SSi leaves have signatures of rapid change of metabolism and signaling, followed by later induction of defense genes...
  16. Firth J, Ekuni D, Irie K, Tomofuji T, Morita M, Putnins E. Lipopolysaccharide induces a stromal-epithelial signalling axis in a rat model of chronic periodontitis. J Clin Periodontol. 2013;40:8-17 pubmed publisher
    ..These results establish a periodontitis model for studying gene product interactions and suggests that the onset of junctional epithelial disease hyperproliferation involves a concerted stromal-epithelial signalling axis. ..
  17. Wong J, Hasan M, Rahman M, Yu A, Chan S, Schaeffer D, et al. Nucleophosmin 1, upregulated in adenomas and cancers of the colon, inhibits p53-mediated cellular senescence. Int J Cancer. 2013;133:1567-77 pubmed publisher
    ..The differential expression of NPM1 along the normal colon-adenoma-carcinoma progression and its involvement in resisting p53 related senescent growth arrest in CRC cell lines implicate its role in supporting CRC tumorigenesis. ..
  18. Janouskovec J, Sobotka R, Lai D, Flegontov P, Konik P, Komenda J, et al. Split photosystem protein, linear-mapping topology, and growth of structural complexity in the plastid genome of Chromera velia. Mol Biol Evol. 2013;30:2447-62 pubmed publisher
  19. Marr N, Wang T, Kam S, Hu Y, Sharma A, Lam A, et al. Attenuation of respiratory syncytial virus-induced and RIG-I-dependent type I IFN responses in human neonates and very young children. J Immunol. 2014;192:948-57 pubmed publisher
    ..Our results suggest that human pDCs are less functional in early life, which may contribute to the increased susceptibility of infants and young children to severe RSV disease. ..
  20. Obeidat M, Nie Y, Fishbane N, Li X, Bosse Y, Joubert P, et al. Integrative Genomics of Emphysema-Associated Genes Reveals Potential Disease Biomarkers. Am J Respir Cell Mol Biol. 2017;57:411-418 pubmed publisher
    ..These results support the use of peripheral blood to detect disease biomarkers. ..
  21. Tripathy S, Toker L, Li B, Crichlow C, Tebaykin D, Mancarci B, et al. Transcriptomic correlates of neuron electrophysiological diversity. PLoS Comput Biol. 2017;13:e1005814 pubmed publisher
    ..Our work highlights the promise and inherent challenges in using cell type-specific transcriptomics to understand the mechanistic origins of neuronal diversity...
  22. Au N, Gown A, Cheang M, Huntsman D, Yorida E, Elliott W, et al. P63 expression in lung carcinoma: a tissue microarray study of 408 cases. Appl Immunohistochem Mol Morphol. 2004;12:240-7 pubmed
    ..These results suggest that p63 may be involved in oncogenesis in a broader range of tumors than was previously thought. ..
  23. Gillis J, Mistry M, Pavlidis P. Gene function analysis in complex data sets using ErmineJ. Nat Protoc. 2010;5:1148-59 pubmed publisher
    ..The protocol should take approximately 1 h, including (one-time) installation and setup. ..
  24. Lockwood W, Stack D, Morris T, Grehan D, O Keane C, Stewart G, et al. Cyclin E1 is amplified and overexpressed in osteosarcoma. J Mol Diagn. 2011;13:289-96 pubmed publisher
    ..Fluorescence in situ hybridization and immunohistochemical analysis confirmed the findings. Overexpression of cyclin E1 has potential prognostic and therapeutic implications that are discussed herein. ..
  25. Shah S, Huang Y, Xu T, Yuen M, Ling J, Ouellette B. Atlas - a data warehouse for integrative bioinformatics. BMC Bioinformatics. 2005;6:34 pubmed
    ..Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/ ..
  26. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques. 2008;45:81-94 pubmed publisher
    ..Analysis of these variants, and previously unannotated splicing events in the HeLa S3 cell line, reveals an overrepresentation of gene categories including those previously implicated in cancer. ..
  27. de la Fuente Nunez C, Korolik V, Bains M, Nguyen U, Breidenstein E, Horsman S, et al. Inhibition of bacterial biofilm formation and swarming motility by a small synthetic cationic peptide. Antimicrob Agents Chemother. 2012;56:2696-704 pubmed publisher
    ..Peptide 1037 shows promise as a potential therapeutic agent against chronic, recurrent biofilm infections caused by a variety of bacteria. ..
  28. Yang Y, Kelly P, Shaffer A, Schmitz R, Yoo H, Liu X, et al. Targeting Non-proteolytic Protein Ubiquitination for the Treatment of Diffuse Large B Cell Lymphoma. Cancer Cell. 2016;29:494-507 pubmed publisher
    ..SMAC mimetics target cIAP1/2 for destruction, and consequently suppress NF-?B and selectively kill BCR-dependent ABC DLBCL lines, supporting their clinical evaluation in patients with ABC DLBCL. ..
  29. Ota T, Gilks C, Longacre T, Leung P, Auersperg N. HOXA7 in epithelial ovarian cancer: interrelationships between differentiation and clinical features. Reprod Sci. 2007;14:605-14 pubmed
    ..HOXA7 staining of tumor cell nuclei is correlated significantly with improved disease-specific survival (P = .0104), which is suggestive of the biological and potentially clinical importance of subcellular HOXA7 localization. ..
  30. Hadaschik B, Ettinger S, Sowery R, Zoubeidi A, Andersen R, Roberge M, et al. Targeting prostate cancer with HTI-286, a synthetic analog of the marine sponge product hemiasterlin. Int J Cancer. 2008;122:2368-76 pubmed publisher
  31. LeBlanc J, Gonçalves E, Mohn W. Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol. 2008;74:2627-36 pubmed publisher
    ..RHA1 cells also induced the biosynthetic pathway for the compatible solute ectoine. These desiccation-specific responses represent the best candidates for important mechanisms of desiccation resistance in RHA1. ..
  32. Liu P, Khurana A, Rattan R, He X, Kalloger S, Dowdy S, et al. Regulation of HSulf-1 expression by variant hepatic nuclear factor 1 in ovarian cancer. Cancer Res. 2009;69:4843-50 pubmed publisher
    ..Collectively, these results indicate that vHNF1 acts as a repressor of HSulf-1 expression and might be a molecular target for ovarian cancer therapy. ..
  33. Morrissy A, Morin R, Delaney A, Zeng T, McDonald H, Jones S, et al. Next-generation tag sequencing for cancer gene expression profiling. Genome Res. 2009;19:1825-35 pubmed publisher
  34. Chiu C, Strugnell S, Griffith O, Jones S, Gown A, Walker B, et al. Diagnostic utility of galectin-3 in thyroid cancer. Am J Pathol. 2010;176:2067-81 pubmed publisher
  35. Desmoulin G, Reno C, Hunter C. Free axial vibrations at 0 to 200 Hz positively affect extracellular matrix messenger ribonucleic acid expression in bovine nucleus pulposi. Spine (Phila Pa 1976). 2010;35:1437-44 pubmed publisher
    ..This may indicate a potential therapeutic stimulus; periodic application of controlled vibration could positively influence matrix maintenance. Further studies on the protein level and long-term effects are warranted. ..
  36. Bhargava A, Mansfield S, Hall H, Douglas C, Ellis B. MYB75 functions in regulation of secondary cell wall formation in the Arabidopsis inflorescence stem. Plant Physiol. 2010;154:1428-38 pubmed publisher
  37. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman S, et al. De novo assembly and analysis of RNA-seq data. Nat Methods. 2010;7:909-12 pubmed publisher
  38. Petit A, Sanders A, Kennedy T, Tetzlaff W, Glattfelder K, Dalley R, et al. Adult spinal cord radial glia display a unique progenitor phenotype. PLoS ONE. 2011;6:e24538 pubmed publisher
    ..Gene ontology analysis highlights potentially unique regulatory pathways that may be further manipulated in SCRG to enhance repair in the context of injury and SC disease. ..
  39. Kam S, Singh A, He J, Ruan J, Gauvreau G, O Byrne P, et al. Peripheral blood gene expression changes during allergen inhalation challenge in atopic asthmatic individuals. J Asthma. 2012;49:219-26 pubmed publisher
  40. Zhang X, Robertson G, Woo S, Hoffman B, Gottardo R. Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. PLoS ONE. 2012;7:e32095 pubmed publisher
  41. Shah S, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486:395-9 pubmed publisher
    ..Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes...
  42. Sehn L. Paramount prognostic factors that guide therapeutic strategies in diffuse large B-cell lymphoma. Hematology Am Soc Hematol Educ Program. 2012;2012:402-9 pubmed publisher
  43. Zhao S, Evans J, Kothari V, Sun G, Larm A, Mondine V, et al. The Landscape of Prognostic Outlier Genes in High-Risk Prostate Cancer. Clin Cancer Res. 2016;22:1777-86 pubmed publisher
  44. El Far M, Kouassi P, Sylla M, Zhang Y, Fouda A, Fabre T, et al. Proinflammatory isoforms of IL-32 as novel and robust biomarkers for control failure in HIV-infected slow progressors. Sci Rep. 2016;6:22902 pubmed publisher
    ..We present here a proof-of-concept for the use of IL-32 as a predictive biomarker for disease progression in SP subjects and identify IL-32 as a potential therapeutic target. ..
  45. Shadeo A, Chari R, Vatcher G, Campbell J, Lonergan K, Matisic J, et al. Comprehensive serial analysis of gene expression of the cervical transcriptome. BMC Genomics. 2007;8:142 pubmed
    ..We demonstrate the utility of this baseline data by identifying genes with aberrant expression in CIN III when compared to normal tissue. ..
  46. Gooderham W, Bains M, McPhee J, Wiegand I, Hancock R. Induction by cationic antimicrobial peptides and involvement in intrinsic polymyxin and antimicrobial peptide resistance, biofilm formation, and swarming motility of PsrA in Pseudomonas aeruginosa. J Bacteriol. 2008;190:5624-34 pubmed publisher
    ..This suggests that PsrA might be a key regulator of antimicrobial peptide resistance and virulence...
  47. Romanuik T, Wang G, Holt R, Jones S, Marra M, Sadar M. Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries. BMC Genomics. 2009;10:476 pubmed publisher
    ..These processes may represent the molecular mechanisms of androgen-dependency of the prostate. Genes that participate in these pathways may be targets for therapies or biomarkers of prostate cancer. ..
  48. Zlosnik J, Speert D. The role of mucoidy in virulence of bacteria from the Burkholderia cepacia complex: a systematic proteomic and transcriptomic analysis. J Infect Dis. 2010;202:770-81 pubmed publisher
  49. Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, et al. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour. 2011;11 Suppl 1:81-92 pubmed publisher
    ..We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar. ..
  50. Antunes L, Wang M, Andersen S, Ferreira R, Kappelhoff R, Han J, et al. Repression of Salmonella enterica phoP expression by small molecules from physiological bile. J Bacteriol. 2012;194:2286-96 pubmed publisher
    ..Due to the critical role of phoP in Salmonella virulence, further studies in this area will likely reveal aspects of the interaction between Salmonella and bile that are relevant to disease...
  51. Minelli C, Dean C, Hind M, Alves A, Amaral A, Siroux V, et al. Association of Forced Vital Capacity with the Developmental Gene NCOR2. PLoS ONE. 2016;11:e0147388 pubmed publisher
    ..Our findings also support SERPINE2, a COPD gene with weak previous evidence of association with FVC, and suggest WNT16 as a further promising candidate. ..
  52. Savoi S, Wong D, Arapitsas P, Miculan M, Bucchetti B, Peterlunger E, et al. Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.). BMC Plant Biol. 2016;16:67 pubmed publisher
  53. Zhang F, Hogue D, Liu L, Fisher C, Hui D, Childs S, et al. M-ABC2, a new human mitochondrial ATP-binding cassette membrane protein. FEBS Lett. 2000;478:89-94 pubmed
    ..The new protein, which is most similar to the mitochondrial (M)-ABC1 protein, was also localized to mitochondria and therefore designated 'M-ABC2'. The N-terminus of M-ABC2 was shown to contain a mitochondrial-targeting signal sequence...
  54. Maines Bandiera S, Huntsman D, Lestou V, Kuo W, Leung P, Horsman R, et al. Epithelio-mesenchymal transition in a neoplastic ovarian epithelial hybrid cell line. Differentiation. 2004;72:150-61 pubmed
  55. Brown N, Vallance B, Coombes B, Valdez Y, Coburn B, Finlay B. Salmonella pathogenicity island 2 is expressed prior to penetrating the intestine. PLoS Pathog. 2005;1:e32 pubmed
    ..This induction of expression precedes any documented SPI-2-dependent phases of typhoid and may be involved in preparing Salmonella to successfully resist the antimicrobial environment encountered within macrophages. ..
  56. Lonergan K, Chari R, DeLeeuw R, Shadeo A, Chi B, Tsao M, et al. Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression. Am J Respir Cell Mol Biol. 2006;35:651-61 pubmed
  57. Healy T, Tymchuk W, Osborne E, Schulte P. Heat shock response of killifish (Fundulus heteroclitus): candidate gene and heterologous microarray approaches. Physiol Genomics. 2010;41:171-84 pubmed publisher
  58. Romanuik T, Wang G, Morozova O, Delaney A, Marra M, Sadar M. LNCaP Atlas: gene expression associated with in vivo progression to castration-recurrent prostate cancer. BMC Med Genomics. 2010;3:43 pubmed publisher
    ..The in vivo gene expression atlas for LNCaP was sequenced and support a role for the androgen receptor in CRPC. ..
  59. Bains M, Fernández L, Hancock R. Phosphate starvation promotes swarming motility and cytotoxicity of Pseudomonas aeruginosa. Appl Environ Microbiol. 2012;78:6762-8 pubmed publisher
    ..This dysregulation also led to increased virulence-associated phenotypes, including swarming motility and cytotoxicity...
  60. Simonsen K, Gallego S, Færgeman N, Kallipolitis B. Strength in numbers: "Omics" studies of C. elegans innate immunity. Virulence. 2012;3:477-84 pubmed publisher
    ..Here, we provide an overview of key aspects of innate immunity in C. elegans revealed by recent whole-genome transcriptomics and proteomics studies of the global response of C. elegans to various bacterial and fungal pathogens. ..
  61. Erho N, Crisan A, Vergara I, Mitra A, Ghadessi M, Buerki C, et al. Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy. PLoS ONE. 2013;8:e66855 pubmed publisher
    ..This early metastasis prediction model based on genomic expression in the primary tumor may be useful for identification of aggressive prostate cancer. ..
  62. Grants J, Ying L, Yoda A, You C, Okano H, Sawa H, et al. The Mediator Kinase Module Restrains Epidermal Growth Factor Receptor Signaling and Represses Vulval Cell Fate Specification in Caenorhabditis elegans. Genetics. 2016;202:583-99 pubmed publisher
    ..Collectively, these data offer an explanation for CKM repression of EGFR signaling output and ectopic vulva formation and provide the first evidence of Mediator CKM-tail module subunit crosstalk in animals. ..
  63. Wang R, Lam P, Liu L, Forrest D, Yousef I, Mignault D, et al. Severe cholestasis induced by cholic acid feeding in knockout mice of sister of P-glycoprotein. Hepatology. 2003;38:1489-99 pubmed
    ..In conclusion, the spgp(-/-) mice provide a unique model to investigate molecular pathways associated with cholestasis and related diseases...
  64. Ruzanov P, Jones S. An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinformatics. 2006;7:193 pubmed
    ..TreeBuilder3D provides a simple interface and has a small size. Written in Java, TreeBuilder3D is a platform-independent, open source application, which may be useful in analysis of large-scale gene expression data. ..
  65. D Souza C, Chopra V, Varhol R, Xie Y, Bohacec S, Zhao Y, et al. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 2008;9:66 pubmed publisher
    ..This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression. ..
  66. Kuchenbauer F, Morin R, Argiropoulos B, Petriv O, Griffith M, Heuser M, et al. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res. 2008;18:1787-97 pubmed publisher
    ..Finally, 55 novel miRNAs species were identified in our data set, adding further complexity to the emerging world of small RNAs. ..
  67. Zulak K, Lippert D, Kuzyk M, Domanski D, Chou T, Borchers C, et al. Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies). Plant J. 2009;60:1015-30 pubmed publisher
  68. Philippe R, Ralph S, K lheim C, Jancsik S, Bohlmann J. Poplar defense against insects: genome analysis, full-length cDNA cloning, and transcriptome and protein analysis of the poplar Kunitz-type protease inhibitor family. New Phytol. 2009;184:865-84 pubmed publisher
  69. Morrissy S, Zhao Y, Delaney A, Asano J, Dhalla N, Li I, et al. Digital gene expression by tag sequencing on the illumina genome analyzer. Curr Protoc Hum Genet. 2010;Chapter 11:Unit 11.11.1-36 pubmed publisher
    ..2009). ..
  70. Chen H, Chow M, Liu C, Lau A, Liu J, Eltis L. Vanillin catabolism in Rhodococcus jostii RHA1. Appl Environ Microbiol. 2012;78:586-8 pubmed publisher
    ..During growth on vanillin or vanillate, vanA was highly upregulated while vdh was not. This study contributes to our understanding of lignin degradation by RHA1 and other actinomycetes...
  71. Dauwe R, Holliday J, Aitken S, Mansfield S. Metabolic dynamics during autumn cold acclimation within and among populations of Sitka spruce (Picea sitchensis). New Phytol. 2012;194:192-205 pubmed publisher
  72. Lam P, Zhao L, McFarlane H, Aiga M, Lam V, Hooker T, et al. RDR1 and SGS3, components of RNA-mediated gene silencing, are required for the regulation of cuticular wax biosynthesis in developing inflorescence stems of Arabidopsis. Plant Physiol. 2012;159:1385-95 pubmed publisher
  73. Mwenifumbo J, Marra M. Cancer genome-sequencing study design. Nat Rev Genet. 2013;14:321-32 pubmed publisher
  74. Bao H, Li E, Mansfield S, Cronk Q, El Kassaby Y, Douglas C. The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. BMC Genomics. 2013;14:359 pubmed publisher
    ..However, little is known about AS patterns in wood-forming tissues and how much AS variation exists within plant populations...
  75. Xia J, Fjell C, Mayer M, Pena O, Wishart D, Hancock R. INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res. 2013;41:W63-70 pubmed publisher
    ..Complex operations are performed through a user-friendly web interface in a step-by-step manner. INMEX is freely available at http://www.inmex.ca. ..
  76. Podder M, Welch W, Zamar R, Tebbutt S. Dynamic variable selection in SNP genotype autocalling from APEX microarray data. BMC Bioinformatics. 2006;7:521 pubmed
    ..In this regard, our method is able to automatically select the probes which work well and reduce the effect of other so-called bad performing probes in a sample-specific manner, for any number of SNPs. ..
  77. Pechkovsky D, Prele C, Wong J, Hogaboam C, McAnulty R, Laurent G, et al. STAT3-mediated signaling dysregulates lung fibroblast-myofibroblast activation and differentiation in UIP/IPF. Am J Pathol. 2012;180:1398-412 pubmed publisher
    ..These data suggest that STAT3 activation regulates several pathways in human LFs associated with normal wound healing, whereas aberrant STAT3 signaling plays a critical role in UIP/IPF pathogenesis. ..
  78. Gusscott S, Kuchenbauer F, Humphries R, Weng A. Notch-mediated repression of miR-223 contributes to IGF1R regulation in T-ALL. Leuk Res. 2012;36:905-11 pubmed publisher
    ..We conclude that miR-223 contributes to IGF1R regulation, but may act in concert with other genes and/or microRNAs to alter T-ALL biology. ..
  79. Zoubarev A, Hamer K, Keshav K, McCarthy E, Santos J, Van Rossum T, et al. Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics. 2012;28:2272-3 pubmed publisher
    ..Web services and integration with third-party resources further increase the scope of the tools, which include a Cytoscape plugin. http://chibi.ubc.ca/Gemma, Apache 2.0 license. ..
  80. Ralph S, Yueh H, Friedmann M, Aeschliman D, Zeznik J, Nelson C, et al. Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large-s. Plant Cell Environ. 2006;29:1545-70 pubmed
    ..Induction of spruce genes of octadecanoid and ethylene signalling, terpenoid biosynthesis, and phenolic secondary metabolism are discussed in more detail...
  81. Brown K, Bylund J, MacDonald K, Song Zhao G, Elliott M, Falsafi R, et al. ROS-deficient monocytes have aberrant gene expression that correlates with inflammatory disorders of chronic granulomatous disease. Clin Immunol. 2008;129:90-102 pubmed publisher
    ..The results are consistent with the hypothesis that ROS are anti-inflammatory mediators that control gene expression and potentially limit the development of sterile inflammatory disorders. ..
  82. Kennah E, Ringrose A, Zhou L, Esmailzadeh S, Qian H, Su M, et al. Identification of tyrosine kinase, HCK, and tumor suppressor, BIN1, as potential mediators of AHI-1 oncogene in primary and transformed CTCL cells. Blood. 2009;113:4646-55 pubmed publisher
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