Browsing HMS Scholarly Articles by Keyword "gene expression"

Now showing items 41-60 of 74

    • Integration of Heterogeneous Expression Data Sets Extends the Role of the Retinol Pathway in Diabetes and Insulin Resistance 

      Park, Peter J.; Kong, Sek Won Won; Tebaldi, Toma; Lai, Weil R.; Kasif, Simon; Kohane, Isaac Samuel (Oxford University Press, 2009)
      Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project ...

    • Integrative network analysis reveals molecular mechanisms of blood pressure regulation 

      Huan, Tianxiao; Meng, Qingying; Saleh, Mohamed A; Norlander, Allison E; Joehanes, Roby; Zhu, Jun; Chen, Brian H; Zhang, Bin; Johnson, Andrew D; Ying, Saixia; Courchesne, Paul; Raghavachari, Nalini; Wang, Richard; Liu, Poching; O'Donnell, Christopher J; Vasan, Ramachandran; Munson, Peter J; Madhur, Meena S; Harrison, David G; Yang, Xia; Levy, Daniel (BlackWell Publishing Ltd, 2015)
      Genome-wide association studies (GWAS) have identified numerous loci associated with blood pressure (BP). The molecular mechanisms underlying BP regulation, however, remain unclear. We investigated BP-associated molecular ...

    • Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production 

      Colijn, Caroline; Brandes, Aaron; Zucker, Jeremy Daniel Hofeld; Lun, Desmond S.; Weiner, Brian; Farhat, Maha Reda; Cheng, Tan-Yun; Moody, D Branch; Murray, Megan Blanche; Galagan, James E (Public Library of Science, 2009)
      Metabolism is central to cell physiology, and metabolic disturbances play a role in numerous disease states. Despite its importance, the ability to study metabolism at a global scale using genomic technologies is limited. ...

    • A Latent Pro-Survival Function for the Mir-290-295 Cluster in Mouse Embryonic Stem Cells 

      Zheng, Grace X. Y.; Medeiros, Lea A.; Kirak, Oktay; Dennis, Lucas M.; Jaenisch, Rudolf; Burge, Christopher B.; Ravi, Arvind; Calabrese, Joseph Michael; McManus, Michael Louis; Sharp, Phillip A. (Public Library of Science, 2011)
      MicroRNAs (miRNAs) post-transcriptionally regulate the expression of thousands of distinct mRNAs. While some regulatory interactions help to maintain basal cellular functions, others are likely relevant in more specific ...

    • LPA5 Is Abundantly Expressed by Human Mast Cells and Important for Lysophosphatidic Acid Induced MIP-1β Release 

      Lundequist, Anders; Boyce, Joshua A. (Public Library of Science, 2011)
      Background: Lysophosphatidic acid (LPA) is a bioactive lipid inducing proliferation, differentiation as well as cytokine release by mast cells through G-protein coupled receptors. Recently GPR92/LPA5 was identified as an ...

    • Metabolic Pathway Signatures Associated with Urinary Metabolite Biomarkers Differentiate Bladder Cancer Patients from Healthy Controls 

      Kim, Won Tae; Yun, Seok Joong; Yan, Chunri; Jeong, Pildu; Kim, Ye Hwan; Lee, Il-Seok; Kang, Ho-Won; Park, Sunghyouk; Moon, Sung-Kwon; Choi, Yung-Hyun; Choi, Young Deuk; Kim, Isaac Yi; Kim, Jayoung; Kim, Wun-Jae (Yonsei University College of Medicine, 2016)
      Purpose Our previous high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry study identified bladder cancer (BCA)-specific urine metabolites, including carnitine, acylcarnitines, and melatonin. ...

    • MicroRNA-Mediated mRNA Translation Activation in Quiescent Cells and Oocytes Involves Recruitment of a Nuclear microRNP 

      Truesdell, S. S.; Mortensen, R. D.; Seo, M.; Schroeder, J. C.; Lee, J. H.; LeTonqueze, O.; Vasudevan, Shobha (Nature Publishing Group, 2012)
      MicroRNAs can promote translation of specific mRNAs in quiescent (G0) mammalian cells and immature Xenopus laevis oocytes. We report that microRNA-mediated upregulation of target mRNAs in oocytes is dependent on nuclear ...

    • miRNA Profiling of Naïve, Effector and Memory CD8 T Cells 

      Wu, Haoquan; Neilson, Joel R.; Kumar, Priti; Manocha, Monika; Shankar, Premlata; Sharp, Phillip A.; Manjunath, N. (Public Library of Science, 2007)
      microRNAs have recently emerged as master regulators of gene expression during development and cell differentiation. Although profound changes in gene expression also occur during antigen-induced T cell differentiation, ...

    • Molecular stratification of metastatic melanoma using gene expression profiling : Prediction of survival outcome and benefit from molecular targeted therapy 

      Cirenajwis, Helena; Ekedahl, Henrik; Lauss, Martin; Harbst, Katja; Carneiro, Ana; Enoksson, Jens; Rosengren, Frida; Werner-Hartman, Linda; Törngren, Therese; Kvist, Anders; Fredlund, Erik; Bendahl, Pär-Ola; Jirström, Karin; Lundgren, Lotta; Howlin, Jillian; Borg, Åke; Gruvberger-Saal, Sofia K.; Saal, Lao H.; Nielsen, Kari; Ringnér, Markus; Tsao, Hensin; Olsson, Håkan; Ingvar, Christian; Staaf, Johan; Jönsson, Göran (Impact Journals LLC, 2015)
      Melanoma is currently divided on a genetic level according to mutational status. However, this classification does not optimally predict prognosis. In prior studies, we have defined gene expression phenotypes (high-immune, ...

    • Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study 

      Hägg, Sara; Skogsberg, Josefin; Lundström, Jesper; Noori, Peri; Nilsson, Roland; Zhong, Hua; Maleki, Shohreh; Shang, Ming-Mei; Brinne, Björn; Bradshaw, Maria; Bajic, Vladimir B.; Samnegård, Ann; Silveira, Angela; Gigante, Bruna; Leander, Karin; de Faire, Ulf; Rosfors, Stefan; Lockowandt, Ulf; Liska, Jan; Konrad, Peter; Takolander, Rabbe; Franco-Cereceda, Anders; Schadt, Eric E.; Ivert, Torbjörn; Hamsten, Anders; Tegnér, Jesper; Björkegren, Johan; Kerr, Kathleen; Kaplan, Lee Michael (Public Library of Science, 2009)
      Environmental exposures filtered through the genetic make-up of each individual alter the transcriptional repertoire in organs central to metabolic homeostasis, thereby affecting arterial lipid accumulation, inflammation, ...

    • Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk 

      Kar, S. P.; Tyrer, J. P.; Li, Qiyuan; Lawrenson, K.; Aben, K. K. H.; Anton-Culver, H.; Antonenkova, N.; Chenevix-Trench, G.; Baker, H.; Bandera, E. V.; Bean, Y. T.; Beckmann, M. W.; Berchuck, A.; Bisogna, M.; Bjorge, L.; Bogdanova, N.; Brinton, L.; Brooks-Wilson, A.; Butzow, R.; Campbell, I.; Carty, K.; Chang-Claude, J.; Chen, Y. A.; Chen, Z.; Cook, L. S.; Cramer, Daniel William; Cunningham, J. M.; Cybulski, C.; Dansonka-Mieszkowska, A.; Dennis, J.; Dicks, E.; Doherty, J. A.; Dork, T.; du Bois, A.; Durst, M.; Eccles, D.; Easton, D. F.; Edwards, R. P.; Ekici, A. B.; Fasching, P. A.; Fridley, B. L.; Gao, Y.-T.; Gentry-Maharaj, A.; Giles, G. G.; Glasspool, R.; Goode, E. L.; Goodman, M. T.; Grownwald, J.; Harrington, P.; Harter, P.; Hein, A.; Heitz, F.; Hildebrandt, M. A. T.; Hillemanns, P.; Hogdall, E.; Hogdall, C. K.; Hosono, S.; Iversen, E. S.; Jakubowska, A.; Paul, J.; Jensen, A.; Ji, B.-T.; Karlan, B. Y.; Kjaer, S. K.; Kelemen, L. E.; Kellar, M.; Kelley, J.; Kiemeney, L. A.; Krakstad, C.; Kupryjanczyk, J.; Lambrechts, D.; Lambrechts, S.; Le, N. D.; Lee, A. W.; Lele, S.; Leminen, A.; Lester, J.; Levine, D. A.; Liang, D.; Lissowska, J.; Lu, K.; Lubinski, J.; Lundvall, L.; Massuger, L.; Matsuo, K.; McGuire, V.; McLaughlin, J. R.; McNeish, I. A.; Menon, U.; Modugno, F.; Moysich, K. B.; Narod, S. A.; Nedergaard, L.; Ness, R. B.; Nevanlinna, H.; Odunsi, K.; Olson, S. H.; Orlow, I.; Orsulic, S.; Weber, R. P.; Pearce, C. L.; Pejovic, T.; Pelttari, L. M.; Permuth-Wey, J.; Phelan, C. M.; Pike, M. C.; Poole, Elizabeth M.; Ramus, S. J.; Risch, H. A.; Rosen, B.; Rossing, M. A.; Rothstein, J. H.; Rudolph, A.; Runnebaum, I. B.; Rzepecka, I. K.; Salvesen, H. B.; Schildkraut, J. M.; Schwaab, I.; Shu, X.-O.; Shvetsov, Y. B.; Siddiqui, N.; Sieh, W.; Song, H.; Southey, M. C.; Sucheston-Campbell, L. E.; Tangen, I. L.; Teo, S.-H.; Terry, Kathryn Lynne; Thompson, P. J.; Timorek, A.; Tsai, Y.-Y.; Tworoger, Shelley Slate; van Altena, A. M.; Van Nieuwenhuysen, E.; Vergote, I.; Vierkant, R. A.; Wang-Gohrke, S.; Walsh, C.; Wentzensen, N.; Whittemore, A. S.; Wicklund, K. G.; Wilkens, L. R.; Woo, Y.-L.; Wu, X.; Wu, A.; Yang, H.; Zheng, W.; Ziogas, A.; Sellers, T. A.; Monteiro, A. N. A.; Freedman, M. L.; Gayther, S. A.; Pharoah, P. D. P. (American Association for Cancer Research (AACR), 2015)
      BACKGROUND: Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription ...

    • A Novel SALL4/OCT4 Transcriptional Feedback Network for Pluripotency of Embryonic Stem Cells 

      Yang, Jianchang; Ma, Yupo; Bridger, Joanna Mary; Gao, Chong; Chai, Li (Public Library of Science, 2010)
      Background: SALL4 is a member of the SALL gene family that encodes a group of putative developmental transcription factors. Murine Sall4 plays a critical role in maintaining embryonic stem cell (ES cell) pluripotency and ...

    • Novel Secretion Apparatus Maintains Spore Integrity and Developmental Gene Expression in Bacillus subtilis 

      Doan, Thierry; Morlot, Cecile; Meisner, Jeffrey; Serrano, Monica; Henriques, Adriano O.; Moran, Charles P. Jr.; Rudner, David Z. (Public Library of Science, 2009)
      Sporulation in Bacillus subtilis involves two cells that follow separate but coordinately regulated developmental programs. Late in sporulation, the developing spore (the forespore) resides within a mother cell. The ...

    • Organotypic Culture of Physiologically Functional Adult Mammalian Retinas 

      Koizumi, Amane; Zeck, Günther; Ben, Yixin; Masland, Richard Harry; Jakobs, Tatjana Claudia (Public Library of Science, 2007)
      Background: The adult mammalian retina is an important model in research on the central nervous system. Many experiments require the combined use of genetic manipulation, imaging, and electrophysiological recording, which ...

    • Oxidative Stress Impairs the Heat Stress Response and Delays Unfolded Protein Recovery 

      Adachi, Masaaki; Liu, Yaohua; Fujii, Kyoko; Calderwood, Stuart K.; Nakai, Akira; Imai, Kohzoh; Shinomura, Yasuhisa (Public Library of Science, 2009)
      Background: Environmental changes, air pollution and ozone depletion are increasing oxidative stress, and global warming threatens health by heat stress. We now face a high risk of simultaneous exposure to heat and oxidative ...

    • Patterns of \(Cis\) Regulatory Variation in Diverse Human Populations 

      Montgomery, Stephen B.; Dimas, Antigone S.; Parts, Leopold; Stegle, Oliver; Ingle, Catherine E.; Sekowska, Magda; Gutierrez-Arcelus, Maria; Nisbett, James; Nica, Alexandra C.; Beazley, Claude; Durbin, Richard; Deloukas, Panos; Dermitzakis, Emmanouil T.; Stranger, Barbara Elaine; Smith, George W.; Price, Alkes; Raj, Towfique (Public Library of Science, 2012)
      The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. ...

    • Phenotypic Switching of Nonpeptidergic Cutaneous Sensory Neurons Following Peripheral Nerve Injury 

      Wang, Ting; Molliver, Derek C.; Jing, Xiaotang; Schwartz, Erica S.; Yang, Fu-Chia; Samad, Omar Abdel; Ma, Qiufu; Davis, Brian M. (Public Library of Science, 2011)
      In adult mammals, the phenotype of half of all pain-sensing (nociceptive) sensory neurons is tonically modulated by growth factors in the glial cell line-derived neurotrophic factor (GDNF) family that includes GDNF, artemin ...

    • The Physiological Period Length of the Human Circadian Clock In Vivo is Directly Proportional to Period in Human Fibroblasts 

      Pagani, Lucia; Semenova, Ekaterina A.; Moriggi, Ermanno; Revell, Victoria L.; Hack, Lisa M.; Arendt, Josephine; Skene, Debra J.; Meier, Fides; Izakovic, Jan; Wirz-Justice, Anna; Cajochen, Christian; Sergeeva, Oksana J.; Cheresiz, Sergei V.; Danilenko, Konstantin V.; Eckert, Anne; Reif, Andreas; Lockley, Steven Ward; Brown, Steven A. (Public Library of Science, 2010)
      Background: Diurnal behavior in humans is governed by the period length of a circadian clock in the suprachiasmatic nuclei of the brain hypothalamus. Nevertheless, the cell-intrinsic mechanism of this clock is present in ...

    • Power Enhancement Via Multivariate Outlier Testing With Gene Expression Arrays 

      Asare, Adam L.; Gao, Zhong; Carey, Vincent James; Wang, Richard; Seyfert-Margolis, Vicki (Oxford University Press, 2008)
      Motivation: As the use of microarrays in human studies continues to increase, stringent quality assurance is necessary to ensure accurate experimental interpretation. We present a formal approach for microarray quality ...

    • A Practical Platform for Blood Biomarker Study by Using Global Gene Expression Profiling of Peripheral Whole Blood 

      Tian, Ze; Palmer, Nathan; Schmid, Patrick; Yao, Hui; Galdzicki, Michal; Berger, Bonnie; Wu, Erxi; Kohane, Isaac Samuel (Public Library of Science, 2009)
      Background: Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression ...