Publications using Ariadne Software
Pathway Analysis [119]
Analysis of gene expression microarray data [165]
Analysis of proteomics data [12]
Drug discovery [24]
Disease mechanism [106]
Human genetics [10]
Toxicogenomics [7]
Text mining [8]
Model organisms [10]
Databases [3]
Plants [1]
Reviews [13]
Websites [5]
Publications by Ariadne authors [21]
Patents [33]
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The first five years of the Wnt targetome Vlad, A.,Rohrs, S.,Klein-Hitpass, L.,Muller, O. Cellular Signalling, 20 (5), p.795-802, Product: Pathway Studio |
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Phenotype reversion in fetal human liver epithelial cells identifies the role of an intermediate meso-endodermal stage before hepatic maturation Mari Inada, Antonia Follenzi, Kang Cheng, Manju Surana, Brigid Joseph, Daniel Benten, Sriram Bandi, Hong Qian, and Sanjeev Gupta J. Cell Sci., Mar 2008; 10.1242/jcs.019315, Product: Pathway Studio |
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Transcriptional Adaptation to Clcn5 Knockout in Proximal Tubules of the Mouse Kidney Jerry Wright, Marcelo M. Morales, Jackson Sousa-Menzes, Debora Ornellas, Jennifer Sipes, and Sandra E. Guggino Physiol Genomics, Mar 2008; 10.1152/physiolgenomics.00024.2008, Product: PathwayAssist |
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Chemical rescue of DF508-CFTR mimics genetic repair in cystic fibrosis bronchial epithelial cells Om V. Singh, Harvey B. Pollard, and Pamela L. Zeitlin Mol. Cell. Proteomics, Feb 2008; 10.1074/mcp.M700303-MCP200, Product: Pathway Studio |
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Scan of 977 nonsynonymous SNPs in CLL4 trial patients for the identification of genetic variants influencing prognosis Gabrielle S. Sellick, Rachel Wade, Susan Richards, David G. Oscier, Daniel Catovsky, and Richard S. Houlston Blood, Feb 2008; 111: 1625 - 1633, Product: PathwayAssist |
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Bioinformatics applications for pathway analysis of microarray data Werner, T Current Opinion in Biotechnology, 19 (1), p.50-54, Product: Pathway Studio |
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Harnessing genetically engineered mouse models for preclinical testing Robles, A.I., Varticovski, L. Chemico-Biological Interactions, 171 (2), p.159-164, Product: Pathway Studio |
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Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia Peter F. Dunfield, Anton Yuryev, Pavel Senin, Angela V. Smirnova, Matthew B. Stott, Shaobin Hou, Binh Ly, Jimmy H. Saw, Zhemin Zhou, Yan Ren, Jianmei Wang, Bruce W. Mountain, Michelle A. Crowe, Tina M. Weatherby, Paul L. E. Bodelier, Werner Liesack, Lu Feng, Lei Wang, Maqsudul Alam Nature 450, 879 - 882 (06 Dec 2007), Product: Pathway Studio, Topic: Applications of pathway analysis |
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cAMP Response Element-Binding Protein-Mediated Gene Expression Increases the Intrinsic Excitability of CA1 Pyramidal Neurons Mikel Lopez de Armentia, Dragana Jancic, Roman Olivares, Juan M. Alarcon, Eric R. Kandel, and Angel Barco J. Neurosci., Dec 2007; 27: 13909 - 13918., Product: Pathway Studio |
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A network-based approach to the analysis of acute wound healing N.B. Menke, K.R. Ward and R.F. Diegelmann Journal of Critical Care, Vol.22(4) 2007 p332, Product: Pathway Studio |
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Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells Yan Xu , Machiko Ikegami , Yanhua Wang , Yohei Matsuzaki and Jeffrey A Whitsett BMC Genomics 2007, 8:455, Product: Pathway Studio |
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Predicting aging/longevity-related genes in the nematode Caenorhabditis elegans. Witten TM, Bonchev D. Chem Biodivers. 2007 Nov;4(11):2639-55., Product: Pathway Studio |
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Genomic Changes in Regenerated Porcine Coronary Arterial Endothelial Cells Mary Y.K. Lee, Hung-Fat Tse, Chung-Wah Siu, Shu-Guang Zhu, Ricky Y.K. Man, and Paul M. Vanhoutte Arterioscler. Thromb. Vasc. Biol., Nov 2007; 27: 2443 - 2449, Product: PathwayAssist |
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Genomic and Nongenomic Effects of Estrogen Signaling in Human Endometrial Cells: Involvement of the Growth Factor Receptor Signaling Downstream AKT Pathway Sussane C. J. P. Gielen, Lindy A. M. Santegoets, Liesbeth C. M. Khne, Wilfred F. J. Van IJcken, Bianca Boers-Sijmons, Payman Hanifi-Moghaddam, Theo J. M. Helmerhorst, Leen J. Blok, and Curt W. Burger Reproductive Sciences, Vol. 14, No. 7, 646-654 (2007), Product: Pathway Studio |
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Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. BMC Bioinformatics. 2007 Jul 10;8(1):243, Product: MedScan, Topic: MedScan, Pathway and function |
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Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes Tracy M Clement, Matthew D Anway, Mehmet Uzumcu, and Michael K Skinner Reproduction, Sep 2007; 134: 455 - 472, Product: PathwayAssist |
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The PPAR resource page John P. Vanden Heuvel BBA - Molecular and Cell Biology of Lipids, 1771 (8), p.1108-1112, Aug 2007, Product: Pathway Studio |
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A novel computational approach to the genetics of polycystic ovarian syndrome (PCOS) M. Nam Menke, N.B. Menke, D.G. Bonchev, T.M. Witten, J.R. Wood and J.F. Straussa Fertility and Sterility, v. 88, Supp.1, Page S73, Product: Pathway Studio |
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Molecular signatures of trauma-hemorrhagic shock-induced lung injury: hemorrhage- and injury-associated genes. R Feinman, EA Deitch, V Aris, HB Chu, B Abungu, FJ Caputo, A Galante, D Xu, Q Lu, I Colorado, D Streck, J Dermody, and P Soteropoulos Shock. 2007 Sep;28(3):360-8, Product: PathwayAssist |
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Propagation of large concentration changes in reversible protein-binding networks Maslov S, Ispolatov I. Proc Natl Acad Sci U S A. 2007, Product: None, Topic: Network topology and dynamics |
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Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions Ekaterina Kotelnikova, Andrey Kalinin, Anton Yuryev, and Sergei Maslov Evolutionary Bioinformatics, Product: MedScan, Topic: Network evolution |
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Transcriptome teleonomy and scavenger lipidomics of albumin and alpha 1-acid glycoproteins: contextual genome-wide ontology enrichment as evidence for the epigenetic code? Pauli Ojala, , Sami Kilpinen, Lotta Arola, Petri Trnen, Elmar Bucher, Kalle Ojala, Kristiina Iljin, Mari Peltonen, Rolf Skotheim, Kristine Kleivi, Martti Tolvanen, Reija Autio, Pentti Somerharju, Olli Kallioniemi and Saara Laitinen Physics of Lipids, 149, p.S86-S86, Sep 2007, Product: Pathway Studio |
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Profiling Studies in Ovarian Cancer: A Review Rudolf S. N. Fehrmann, Xiang-yi Li, Ate G. J. van der Zee, Steven de Jong, Gerard J. te Meerman, Elisabeth G. E. de Vries, and Anne P. G. Crijns Oncologist, Aug 2007; 12: 960 - 966, Product: PathwayAssist |
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Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model Sachiyo Aburatani, Fuyan Sun, Shigeru Saito, Masao Honda, Shu-Ichi Kaneko, and Katsuhisa Horimoto EURASIP J Bioinform Syst Biol. 2007; 2007: 47214, Product: PathwayAssist |
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Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins A Budhu, Y Chen, J.W. Kim, M Forgues, K Valerie, C.C. Harris, and X.W. Wang Carcinogenesis, Product: PathwayAssist |
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Transcriptional network governing the angiogenic switch in human pancreatic cancer Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, Hauser K, Hahnfeldt P, Hlatky L, Debus J, Peters JM, Friess H, Folkman J, Huber PE. Proc Natl Acad Sci U S A. 2007 Jul 24, Product: Pathway Studio |
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Exenatide blocks JAK1-STAT1 in pancreatic beta cells Couto FM, Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Hanson M, Fernandez LA, Wang P, Kendziorski C, Shalev A Metabolism. 2007 Jul;56(7):915-8, Product: Pathway Studio |
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Neutrophils: the forgotten cell in JIA disease pathogenesis James N Jarvis, Kaiyu Jiang, Howard R Petty, and Michael Centola Pediatr Rheumatol Online J. 2007; 5: 13., Product: Pathway Studio |
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Identification of human cell responses to benzene and benzene metabolites Bruce Gillis, Igor M. Gavin, Zarema Arbieva, Stephen T. King, Sundararajan Jayaraman, Bellur S. Prabhakar Genomics, Product: Pathway Studio, ResNet |
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Gap junction and purinergic P2 receptor proteins as a functional unit: insights from transcriptomics. Iacobas DA, Suadicani SO, Iacobas S, Chrisman C, Cohen MA, Spray DC, Scemes E. J Membr Biol. 2007 Jun;217(1-3):83-91, Product: Pathway Studio |
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Pathway analysis for design of promiscuous drugs and selective drug mixtures. Sivachenko A, Kalinin A, Yuryev A. Curr Drug Discov Technol. 2006 Dec;3(4):269-77., Product: Pathway Studio, Topic: Applications of pathway analysis |
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Molecular networks in microarray analysis. Sivachenko AY, Yuryev A, Daraselia N, Mazo I. J Bioinform Comput Biol., Product: Pathway Studio, Topic: Gene expression analysis |
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Specific Activation of the Glucocorticoid Receptor and Modulation of Signal Transduction Pathways in Human Lens Epithelial Cells Vanita Gupta, Niranjan Awasthi, and B. J. Wagner Invest. Ophthalmol. Vis. Sci., Apr 2007; 48: 1724 - 1734., Product: PathwayAssist |
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Functional genomics and proteomics of the cellular osmotic stress response in `non-model\' organisms Dietmar Kltz, Diego Fiol, Nelly Valkova, Silvia Gomez-Jimenez, Stephanie Y. Chan, and Jinoo Lee J. Exp. Biol., May 2007; 210: 1593 - 1601, Product: Pathway Studio |
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Pathway analysis software as a tool for drug target selection, prioritization and validation of drug mechanism Sivachenko A & Yuryev A Expert Opinion on Therapeutic Targets, v.11(3), pp.411-421, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation Peter G. Fuhrken, Chi Chen, William M. Millera, and Eleftherios T. Papoutsakis Experimental Hematology,V.35(3):476-489.e23, Product: Pathway Studio |
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The microglial gene regulatory network activated by interferon-gamma Moran, L.B.,Duke, D.C.,Graeber, M.B. Journal of Neuroimmunology, Feb 2007, Product: Pathway Studio |
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A cassette system to study ES cell differentiation by inducible RNA interference Daniel Wegmller, Ines Raineri, Brigitte Gross, Edward J. Oakeley, and Christoph Moroni Stem Cells, Jan 2007; 10.1634/stemcells.2006-0106., Product: Pathway Studio |
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Overexpression of Angiopoietin-like Protein 4 Alters Mitochondria Activities and Modulates Methionine Metabolic Cycle in the Liver Tissues of db/db Diabetic Mice Yu Wang, Karen SL Lam, Janice BB Lam, Michael C Lam, Priscilla TY Leung, Mingyan Zhou, and Aimin Xu Molecular Endocrinology, doi:10.1210/me.2006-0249, Product: Pathway Studio |
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Microarrays in breast cancer research and clinical practice the future lies ahead Sofia K Gruvberger-Saal, Heather E Cunliffe, Kristen M Carr and Ingrid A Hedenfalk Endocrine-Related Cancer, Product: Pathway Studio |
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Phenotypic and global gene expression profile changes between low passage and high passage MIN-6 cells Lorraine O Driscoll, Patrick Gammell, Eadaoin McKiernan, Eoin Ryan, Per Bendix Jeppesen, Sweta Rani, and Martin Clynes J. Endocrinol., Dec 2006; 191: 665 - 676, Product: PathwayAssist |
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Data Mining for Gene Networks Relevant to Poor Prognosis in Lung Cancer Via Backward-Chaining Rule Induction Mary E. Edgerton, Douglas H. Fisher, Lianhong Tang,Lewis J. Frey, Zhihua Chen Cancer Informatics 2006:2, Product: Pathway Studio |
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RET oncoproteins induce tyrosine phosphorylation changes of proteins involved in RNA metabolism L. Gorlaa, M. Canta, F. Miccicha, C. Patellia, P. Mondellinia, M.A. Pierottia, and I. Bongarzonea Cellular Signalling V.18(12):2272-2282, Product: Pathway Studio |
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Integrated molecular profiling of SOD2 expression in multiple myeloma Elaine M Hurt, Suneetha B Thomas, Benjamin Peng, and William L Farrar Blood, Dec 2006; 10.1182/blood-2006-07-035162., Product: PathwayAssist |
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Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms Kai Xia, Huiling Xue, Dong Dong, Shanshan Zhu, Jiamu Wang, Qingpeng Zhang, Lei Hou, Hua Chen, Ran Tao, Zheng Huang, Zheng Fu, Ye-Guang Chen, Jing-Dong J. Han PLoS Comput Biol, Product: Pathway Studio |
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Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression Fernando O. Martinez, Siamon Gordon, Massimo Locati, and Alberto Mantovani J. Immunol., Nov 2006; 177: 7303 - 7311, Product: Pathway Studio |
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Peroxisome Proliferator-Activated Receptor Is Highly Expressed in Pancreatic Cancer and Is Associated With Shorter Overall Survival Times Glen Kristiansen, Juliane Jacob, Ann-Christin Buckendahl, Robert Grtzmann, Ingo Alldinger, Bence Sipos, Gnter Klppel, Marcus Bahra, Jan M. Langrehr, Peter Neuhaus, Manfred Dietel, and Christian Pilarsky Clin. Cancer Res., Nov 2006; 12: 6444 - 6451., Product: PathwayAssist |
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Essential role of Jun family transcription factors in PU.1 knockdown induced leukemic stem cells Ulrich Steidl, Frank Rosenbauer, Roel G W Verhaak, Xuesong Gu, Alexander Ebralidze, Hasan H Otu, Steffen Klippel, Christian Steidl, Ingmar Bruns, Daniel B Costa, Katharina Wagner, Manuel Aivado, Guido Kobbe, Peter J M Valk, Emmanuelle Passegu, Towia A Libermann, Ruud Delwel, Daniel G Tenen Nature Genetics 38, 1269 - 1277 (01 Nov 2006), Product: Pathway Studio |
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A Sex-Specific Role of Type VII Adenylyl Cyclase in Depression Hines LM, Hoffman PL, Bhave S, Saba L, Kaiser A, Snell L, Goncharov I, LeGault L, Dongier M, Grant B, Pronko S, Martinez L, Yoshimura M, Tabakoff B; World Health Organization/International Society for Biomedical Research on Alcoholism Study on State and Trait Markers of Alcohol Use and Dependence Investigators. The Journal of Neuroscience, Product: PathwayAssist |
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Molecular Network and Chromosomal Clustering of Genes Involved in Synaptic Plasticity in the Hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem, Product: Pathway Studio |
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Time dependent rescue of gene expression by androgens in the mouse proximal caput epididymidis (PC-1) cell line after androgen withdrawal Shayesta Seenundun and Bernard Robaire Endocrinology, Product: Pathway Studio |
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Characterization of differential gene expression profiles in diabetic embryopathy using DNA microarray analysis. Reece EA, Ji I, Wu YK, Zhao Z. Am J Obstet Gynecol. 2006 Oct;195(4):1075-80., Product: Pathway Studio |
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Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling Y F Wong, T H Cheung, K W K Lo, S F Yim, N S S Siu, S C S Chan, T W F Ho, K W Y Wong, M Y Yu, V W Wang, C Li, G J Gardner, T Bonome, W B Johnson, D I Smith, T K H Chung, M J Birrer Oncogene. 2006 Oct 16, Product: Pathway Studio |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (10 Oct 2006), Product: Pathway Studio |
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Search for low penetrance alleles for colorectal cancer through a scan of 1,467 non-synonymous SNPs in 2,575 cases and 2,707 controls with validation by kin-cohort analysis of 14,704 first-degree relatives Webb EL, Rudd MF, Sellick GS, El Galta R, Bethke L, Wood W, Fletcher O, Penegar S, Withey L, Qureshi M, Johnson N, Tomlinson I, Gray R, Peto J, Houlston RS. Hum Mol Genet, Product: PathwayAssist |
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Exercise affects the gene expression profiles of human white blood cells Buettner P, Mosig S, Lechtermann A, Funke H, Mooren FC. J Appl Physiol., Product: PathwayAssist |
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Cluster-based network model for time-course gene expression data Inoue LY, Neira M, Nelson C, Gleave M, Etzioni R. Biostatistics, Product: Pathway Studio |
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Transgenerational Epigenetic Imprinting of the Male Germ-Line by Endocrine Disruptor Exposure During Gonadal Sex Determination Hung-Shu Chang, Matthew D. Anway, Stephen S. Rekow, and Michael K. Skinner Endocrinology, Product: PathwayAssist |
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Systems Biology of AGC Kinases in Fungi Alex Sobko Sci. STKE, Product: Pathway Studio |
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Identification and pathway analysis of immediate hyperosmotic stress responsive molecular mechanisms in tilapia (Oreochromis mossambicus) gill Diego F. Fiola, Stephanie Y. Chana and Dietmar Kltz Comparative Biochemistry and Physiology Part D: Genomics and Proteomics V1(3):344-356, Product: Pathway Studio |
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Cigarette smoke condensate induces cytochromes P450 and aldo-keto reductases in oral cancer cells Nagaraj, N.S. Beckers, S. Mensah, J.K. Waigel, S. Vigneswaran, N. Zacharias, W. Toxicology Letters, Aug 2006, Product: Pathway Studio |
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Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem., Jul 2006; 10.1074/jbc.M605876200., Product: PathwayAssist |
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BiologicalNetworks: visualization and analysis tool for systems biology Michael Baitaluk, Mayya Sedova, Animesh Ray, and Amarnath Gupta Nucleic Acids Res., Jul 2006; 34: W466 - W471., Product: PathwayAssist |
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Targeting transcription factors in cell regulation. Anton Yuryev Expert Opinion on Therapeutic Targets, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Characterization of cell-type specific profiles in tissues and isolated cells from squamous cell carcinomas of the lung Lesleyann Hawthorn, Leighton Stein, Jenniffer Panzarella, Gregory M. Loewen and Heinz Baumann Lung Cancer, 04, 2006, Product: Pathway Studio |
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Signatures of human regulatory T cells: an encounter with old friends and new players. Pfoertner S, Jeron A, Probst-Kepper M, Guzman CA, Hansen W, Westendorf AM, Toepfer T, Schrader AJ, Franzke A, Buer J, Geffers R Genome Biol. 2006 Jun 12;7(7):, Product: Pathway Studio |
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Transcriptional Signatures of Cellular Plasticity in Mice Lacking the {alpha}1 Subunit of GABA-A Receptors Igor Ponomarev, Rajani Maiya, Mark T. Harnett, Gwen L. Schafer, Andrey E. Ryabinin, Yuri A. Blednov, Hitoshi Morikawa, Stephen L. Boehm, II, Gregg E. Homanics, Ari Berman, Kerrie H. Lodowski, Susan E. Bergeson, and R. Adron Harris J. Neurosci., May 2006; 26: 5673 - 5683, Product: PathwayAssist |
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Gene chromosomal organization and expression in cultured human neurons exposed to cocaine and HIV-1 proteins gp120 and tat: drug abuse and NeuroAIDS. Shapshak P, Duncan R, Nath A, Turchan J, Pandjassarame K, Rodriguez H, Duran EM, Ziegler F, Amaro E, Lewis A, Rodriguez A, Minagar A, Davis W, Seth R, Elkomy FF, Chiappelli F, Kazic T. Front Biosci., Product: Pathway Studio |
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Bioinformatics Models In Drug Abuse And NeuroAIDS: Using And Developing Databases Shapshak Paul, Robert Duncan, Jadwiga Turchan, Avindra Nath, Alireza Minagar, Pandjassarame Kangueane, Wade Davis, Francesco Chiappelli, Fatten Elkomy, Raman Seth, Toni Kazic BIOINFORMATION, Product: Pathway Studio |
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A novel prognostic subclass of hepatocellular carcinoma derived from hepatic stem cells. Lee, J-S., Heo, J., Libbrecht, L., Chu, I-S., Kaposi-Novak, P., Calvisi, D. C., Mikaelyan, A., Roberts, L. R., Demetris, A. J., Sun, Z., Nevens, F., Roskams, T., and Thorgeirsson, S. S. Nature Medicine 12(4):410-416, Product: Pathway Studio |
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Variants in the ATM-BRCA2-CHEK2 axis predispose to chronic lymphocytic leukaemia Rudd MF, Sellick GS, Webb EL, Catovsky D, Houlston RS. Blood. 2006 Mar 30, Product: PathwayAssist |
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Quantitative phosphotyrosine proteomics of EphB2 signaling by stable isotope labeling with amino acids in cell culture (SILAC). Zhang G, Spellman DS, Skolnik EY, Neubert TA. J Proteome Res. 2006 Mar;5(3):581-8., Product: Pathway Studio |
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An effective structure learning method for constructing gene networks Xue-wen Chen, Gopalakrishna Anantha, and Xinkun Wang Bioinformatics, Product: PathwayAssist |
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Gene Expression Profiling Reveals the Profound Up-regulation of Hypoxia-Responsive Genes in Primary Human Astrocytes S. M Mense, A. Sengupta, M. Zhou, C. Lan, G. Bentsman, D. J Volsky, and L. Zhang Physiol. Genomics (February 28, 2006)., Product: PathwayAssist |
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A Pathway Analysis of Poly (I:C)-Induced Global Gene Expression Change in Human Peripheral Blood Mononuclear Cells Huang CC, Duffy KE, San Mateo LR, Amegadzie BY, Sarisky RT, Mbow ML. Physiol Genomics. 2006 Mar 22, Product: PathwayAssist |
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Targeted disruption of glycerol kinase gene in mice: expression analysis in liver shows alterations in network partners related to glycerol kinase activity Nicole K. MacLennan, Lola Rahib, Cynthia Shin, Zixing Fang, Steve Horvath, Jason Dean, James C. Liao, Edward R.B. McCabe, and Katrina M. Dipple Hum. Mol. Genet., Feb 2006; 15: 405 - 415., Product: PathwayAssist |
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PathSys: integrating molecular interaction graphs for systems biology Baitaluk, Michael Qian, Xufei Godbole, Shubhada Raval, Alpan Ray, Animesh Gupta, Amarnath BMC Bioinformatics, Feb 2006, Product: Pathway Studio |
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The neuroprotective WldS gene regulates expression of PTTG1 and erythroid differentiation regulator 1-like gene in mice and human cells Gillingwater TH, Wishart TM, Chen PE, Haley JE, Robertson K, MacDonald SH, Middleton S, Wawrowski K, Shipston MJ, Melmed S, Wyllie DJ, Skehel PA, Coleman MP, Ribchester RR. Hum Mol Genet. 2006 Feb 15;15(4):625-35., Product: PathwayAssist |
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Microarray Analysis of Immobilization Stress Triggered Changes in Gene Expression in Rat Adrenal Medulla Esther Louise Sabban, Xiaoping Liu, Richard Kvetnansky, and Lidia I Serova FASEB J, Product: PathwayAssist |
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Pathway Analysis in Drug Development Azat Badretdinov, Anton Yuryev Pharma & Bio Ingridients March 2006, Product: Pathway Studio, Topic: Applications of pathway analysis |
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Automatic pathway building in biological association networks Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia and Ilya Mazo BMC Bioinformatics 2006, 7:171, Product: Pathway Studio, Topic: Pathways and function |
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Androgens Regulate the Immune/Inflammatory Response and Cell Survival Pathways in Rat Ventral Prostate Epithelial Cells A. J. Asirvatham, M. Schmidt, B. Gao, and J. Chaudhary Endocrinology, Jan 2006; 147: 257 - 271., Product: PathwayAssist |
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WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data Yi, Ming Horton, Jay D. Cohen, Jonathan C. Hobbs, Helen H. Stephens, Robert M. BMC Bioinformatics, Jan 2006, Product: Pathway Studio |
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InCeP: Intracellular Pathway Based on mKIAA Protein-Protein Interactions Masatoshi Murakami, Kiyo Shimada, Makoto Kawai, and Hisashi Koga DNA Res, Jan 2006; 10.1093/dnares/dsi014., Product: PathwayAssist |
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Binding properties and evolution of homodimers in protein-protein interaction networks Ispolatov, Iaroslav; Yuryev, Anton; Mazo, Ilya; Maslov, Sergei Nucleic Acids Research 2005 33(11):3629-3635, Product: PathwayAssist, Topic: Network evolution |
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Gene expression profiling in INS-1 cells overexpressing thioredoxin-interacting protein. Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Wang P, Kendziorski C, Shalev A. Biochem Biophys Res Commun. 2005 Oct 28;336(3):770-8., Product: Pathway Studio |
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Analysis off Estrogen Agonism and Antagonism of Tamoxifen, Raloxifene, and ICI182780 in Endometrial Cancer Cells: A Putative Role for the Epidermal Growth Factor Receptor Ligand Amphiregulin Susanne C.J.P. Gielen, Curt W. Burger, Liesbeth C.M. Khne, Payman Hanifi-Moghaddam, and Leen J. Blok Journal of the Society for Gynecologic Investigation, Product: PathwayAssist |
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Nova regulates brain-specific splicing to shape the synapse Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nature Genetics 37, 844-852, Product: Pathway Studio |
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Oncogenic H-Ras Up-regulates Expression of Ku80 to Protect Cells from -Ray Irradiation in NIH3T3 Cells In-Youb Chang, Cha-Kyung Youn, Hong-Beum Kim, Mi-Hwa Kim, Hyun-Ju Cho, Young Yoon, Yun-Sil Lee, Myung-Hee Chung, and Ho Jin You Cancer Res., Aug 2005; 65: 6811 - 6819., Product: PathwayAssist |
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Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses Bjrn Usadel, Axel Nagel, Oliver Thimm, Henning Redestig, Oliver E. Blaesing, Natalia Palacios-Rojas, Joachim Selbig, Jan Hannemann, Maria Conceio Piques, Dirk Steinhauser, Wolf-Rdiger Scheible, Yves Gibon, Rosa Morcuende, Daniel Weicht, Svenja Meyer, and Mark Stitt Plant Physiology, Jul 2005; 138: 1195 - 1204., Product: PathwayAssist |
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Identification of GAS-dependent interferon-sensitive target genes whose transcription is STAT2-dependent but ISGF3-independent Melissa M Brierley, Katie L Marchington, Igor Jurisica and Eleanor N Fish FEBS Journal 273 (2006) 1569-1581, Product: Pathway Studio |
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Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV. Genes, Brain and Behavior, 2006, Product: Pathway Studio |
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Duplication-divergence model of protein interaction network I.Ispolatov, P.L.Krapivsky, A.Yuryev Phys. Rev. E 71, 061911 (2005), Product: Pathway Studio, Topic: Network evolution |
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Transcriptional Basis for Exercise Limitation in Male eNOS Knockout Mice with Age: Heart Failure and the Fetal Phenotype Caroline Ojaimi, Wei Li, Shintaro Kinugawa, Heiner Post, Anna Csiszar, Pal Pacher, Gabor Kaley, and Thomas H Hintze Am J Physiol Heart Circ Physiol, May 2005, Product: PathwayAssist |
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Persistent Nuclear Factor-Kappa-B Activation in Ucp2-/- Mice Leads to Enhanced Nitric Oxide and Inflammatory Cytokine Production Yushi Bai, Hiroki Onuma, Xu Bai, Alexander V. Medvedev, Mary Misukonis, J. Brice Weinberg, Wenhong Cao, Jacques Robidoux, Lisa M. Floering, Kiefer W. Daniel, and Sheila Collins J. Biol. Chem., May 2005, Product: PathwayAssist |
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Comparative gene expression profile of mouse carotid body and adrenal medulla under physiological hypoxia Maria D Ganfornina, M. Teresa Prez-Garca, Gabriel Gutierrez, Eduardo Miguel-Velado, Jos Ramn Lpez-Lpez, Antonio Marin, Diego Sanchez, and Constancio Gonzalez J. Physiol., May 2005, Product: PathwayAssist |
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Pathway analysis of whole genomic expression profiles of colorectal cancer biopsy samples Orsolya Galamb, Ferenc Sipos, Sndor Spisk, Bla Molnr, Andrea Ladnyi, and Zsolt Tulassay AACR Meeting Abstracts, Product: PathwayAssist |
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Alterations of apoptosis in a rhabdomyosarcoma patient with Li-Fraumeni syndrome, familial syndactyly, and absence of germline p53 mutation. Malgorzata Pienkowska, Rika Tsuchida, Elizabeth Sexsmith, Jane Bayani, Gloria Lim, Jeremy A. Squire, and David Malkin AACR Meeting Abstracts, Product: PathwayAssist |
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Identification of genes related to cisplatin-resistance in four isogenic human ovarian cancer cell lines, which only differ in their degree of cisplatin resistance Anne P. G. Crijns, Gert Jan Meersma, Steven De Jong, Gerard J. Te Meerman, Frans Gerbens, Robert M. W. Hofstra, Elisabeth G. E. De Vries and Ate G. J. Van der Zee AACR Meeting Abstracts, Product: PathwayAssist |
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The links between axin and carcinogenesis S Salahshor and J R Woodgett J. Clin. Pathol., Mar 2005; 58: 225 236, Product: PathwayAssist |
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Identifying Local Gene Expression Patterns in Biomolecular Networks A. Y. Sivachenko, A. Yuryev, N. Daraselia, I. Mazo IEEE Computational Systems Bioinformatics Conference, Aug. 8-11, 2005, Product: Pathway Studio, Topic: Gene expression analysis |
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Cliques and duplication-divergence network growth Ispolatov, I ; Krapivsky, P L ; Mazo, I ; Yuryev, A New J.Phys. 7(2005) 145, Product: Pathway Studio, Topic: Network evolution |
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Finding mesoscopic communities in sparse networks I. Ispolatov, I. Mazo, and A. Yuryev J. Stat. Mech. (2006) P09014, Product: Pathway Studio, Topic: Pathways and fucntion |
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Alterations in the Ovarian Transcriptome During Primordial Follicle Assembly and Development Phillip R. Kezele, Jacquelyn M. Ague, Eric Nilsson, and Michael K. Skinner Biol Reprod, Jan 2005, Product: PathwayAssist |
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Osteocyte and Osteoblast Cell Models have Unique Patterns of Gene Expression and Responses to Mechanical Loading Wuchen Yang, Marie A. Harris, Dayong Guo, Lynda F. Bonewald, Stephen E. Harris Department of Periodontics, University of Texas Health Science Center at San Antonio, School of Dentistry, Product: Pathway Studio |
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Microarray analysis of androgen-regulated gene expression in testis: the use of the androgen-binding protein (ABP)-transgenic mouse as a model. Petrusz P, Jeyaraj DA, Grossman G. Reprod Biol Endocrinol. 2005; 3: 70., Product: Pathway Studio |
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Identification of mouse retinal genes differentially regulated by dim and bright cyclic light rearing Hu Huang, Mark Barton Frank, Igor Dozmorov, Wei Cao, Craig Cadwell, Nick Knowlton, Michael Centola and Robert E. Anderson Experimental Eye Research, 2005, Product: Pathway Studio |
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Global Genomic Approaches to the Iron-Regulated Proteome Ying Liu, Zvezdana Popovich and Douglas M. Templeton Ann. Clin. Lab. Sci., Jan 2005; 35: 230 - 239., Product: PathwayAssist |
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Visualizing biological pathways: requirements analysis, systems evaluation and research agenda Purvi Saraiya, Chris North, Karen Duca Information Visualization (2005), 1 15, Product: Pathway Studio |
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Cancer-related pathway collection Tetsuya Shiraishi Sony Computer Science Laboratories, Product: Pathway Studio |
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Impact of Adenoviral Transduction With SREBP1c or AMPK on Pancreatic Islet Gene Expression Profile: Analysis With Oligonucleotide Microarrays Frederique Diraison, Efthimios Motakis, Laura E. Parton, Guy P. Nason, Isabelle Leclerc, and Guy A. Rutter Diabetes, Dec 2004, Product: PathwayAssist |
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Identification of the CREB-binding Protein/p300-interacting Protein CITED2 as a Peroxisome Proliferator-activated Receptor a Coregulator Eric S. Tien, John W. Davis, and John P. Vanden Heuvel J. Biol. Chem., Vol. 279, Issue 23, 24053-24063, June 4, 2004., Product: PathwayAssist |
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Making Mechanistic Connections between Cell Signaling Pathways and Pathological Endpoints Myrtle A. Davis Toxicologic Pathology,Volume 32, Supplement 1 / March-April 2004: 131 135, Product: Pathway Studio |
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Whole genome expression profiling of advance stage papillary serous ovarian cancer reveals activated pathways. Donninger H, Bonome T, Radonovich M, Pise-Masison CA, Brady J, Shih JH, Barrett JC, Birrer MJ. Oncogene. 2004 Sep 13, Product: Pathway Studio |
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FGF-2 enhances the mitotic and chondrogenic potentials of human adult bone marrow-derived mesenchymal stem cells Luis A. Solchaga, Kitsie Penick, John D. Porter, Victor M.Goldberg, Arnold I. Caplan, Jean F. Welter Journal of Cellular Physiology Volume 203, Issue 2, Pages 398 - 409, Nov. 2004, Product: Pathway Studio |
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Long term modulation of gene expression in the mouse eye following laser photocoagulation N. Binz, K. Simpson, W. Y. Shen, C. M. Lai, T. Speed and E.P. Rakoczy Invest Ophthalmol Vis Sci 2004; 45: E-Abstract 2504., Product: PathwayAssist |
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Can Theoretical Analysis of Cellular Regulatory Networks Improve Drug Target Identification and Validation? Burkhard Haefner BUSINESS BRIEFING: FUTURE Drug discovery 2004, Product: Pathway Studio |
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Microarray Data Analysis and Pathway Visualization of Murine Cochlear Ear Hair Cell Differentiation Eric S. Allen & Kris Barbee Submitted on December 4th, 2003, Product: Pathway Studio |
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Pathway studio the analysis and navigation of molecular networks Alexander Nikitin, Sergei Egorov, Nikolai Daraselia, and Ilya Mazo Bioinformatics. 2003 Nov 1;19(16):2155-7, Product: PathwayAssist, Pathway Studio, Topic: Pathway Studio |
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The first five years of the Wnt targetome Vlad, A.,Rohrs, S.,Klein-Hitpass, L.,Muller, O. Cellular Signalling, 20 (5), p.795-802, Product: Pathway Studio |
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Gene Expression Based Recurrence Prediction of Hepatitis B Virus Related Human Hepatocellular Carcinoma Hyun Goo Woo et al Clin. Cancer Res., Apr 2008; 14: 2056 - 2064, Product: Pathway Studio |
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Intestinal tumors adapt to excess dietary iron by altering expression of lipocalin-2 and divalent metal ion transporter James Swain, Chunbiao Li, and Patrick Leahy FASEB J, Mar 2008; 22: 694.3., Product: Pathway Studio |
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Iron supplementation modulates genes involved in oxidoreductase activity, including prostaglandin-endoperoxide synthase 2 in intestinal tumors James Swain, Chunbiao Li, and Patrick Leahy FASEB J, Mar 2008; 22: 692.4, Product: Pathway Studio |
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Network of Paraventricular Nucleus Gene Expression in Angiotensin-salt Hypertension Lihui Yuan, Xia Li, Judith Sved, Alan Sved, Li Liu, and Mohan Raizada FASEB J, Mar 2008; 22: 1168.9, Product: Pathway Studio |
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Gene Expression Networks in Rostral Ventrolateral Medulla (RVLM) of Rats with Angiotensin-salt Hypertension Lihui Yuan, Xia Li, Judith Sved, Alan Sved, Mohan Raizada, and Li Liu FASEB J, Mar 2008; 22: 1168.10, Product: Pathway Studio |
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Phenotype reversion in fetal human liver epithelial cells identifies the role of an intermediate meso-endodermal stage before hepatic maturation Mari Inada, Antonia Follenzi, Kang Cheng, Manju Surana, Brigid Joseph, Daniel Benten, Sriram Bandi, Hong Qian, and Sanjeev Gupta J. Cell Sci., Mar 2008; 10.1242/jcs.019315, Product: Pathway Studio |
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Towards a pathway definition of Parkinson s disease: a complex disorder with links to cancer, diabetes and inflammation Linda B. Moran and Manuel B. Graeber Neurogenetics, Vol.9(1)2008, Product: Pathway Studio |
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IFN-beta-regulated genes show abnormal expression in therapy-nave relapsing remitting MS mononuclear cells: Gene expression analysis employing all reported protein protein interactions Ken D. Yamaguchi, Daniel L. Ruderman, Ed Croze, T. Charis Wagner, Sharlene Velichko, Anthony T. Reder, Hugh Salamon J Neuroimmunol. 2008 Feb 13, Product: Pathway Studio, ResNet |
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Bioinformatics applications for pathway analysis of microarray data Werner, T Current Opinion in Biotechnology, 19 (1), p.50-54, Product: Pathway Studio |
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Early Events in the Pathogenesis of Epithelial Ovarian Cancer Charles N. Landen, Jr, Michael J. Birrer, and Anil K. Sood J. Clin. Oncol., Jan 2008; 10.1200/JCO.2006.07.9970., Product: Pathway Studio |
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The tale of two domains: Proteomic and genomic analysis of SMYD2, a new histone methyltransferase Mohamed Abu-Farha, Jean-Philippe Lambert, Ashraf S. Al-Madhoun, Fred Elisma, Ilona S. Skerjanc, and Daniel Figeys Mol. Cell. Proteomics, Dec 2007; 10.1074/mcp.M700271-MCP200, Product: Pathway Studio |
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cAMP Response Element-Binding Protein-Mediated Gene Expression Increases the Intrinsic Excitability of CA1 Pyramidal Neurons Mikel Lopez de Armentia, Dragana Jancic, Roman Olivares, Juan M. Alarcon, Eric R. Kandel, and Angel Barco J. Neurosci., Dec 2007; 27: 13909 - 13918., Product: Pathway Studio |
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Dexamethasone Sensitizes the Neonatal Intestine to Fructose Induction of Intestinal Fructose Transporter (Slc2A5) Function Veronique Douard, Xue-Lin Cui, Patricia Soteropoulos, and Ronaldo P. Ferraris Endocrinology, Jan 2008; 149: 409 - 423, Product: PathwayAssist |
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Gene Expression in Human Hippocampus from Cocaine Abusers Identifies Genes which Regulate Extracellular Matrix Remodeling Deborah C. Mash, Jarlath ffrench-Mullen, Nikhil Adi, Yujing Qin, Andrew Buck, and John Pablo PLoS ONE. 2007; 2(11): e1187, Product: Pathway Studio |
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Microarray data analysis and mining approaches Francesca Cordero, Marco Botta, and Raffaele A. Calogero Brief Funct Genomic Proteomic, Dec 2007; 6: 265 - 281, Product: Pathway Studio |
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Gene expression and biological processes influenced by deletion of Stat3 in pulmonary type II epithelial cells Yan Xu , Machiko Ikegami , Yanhua Wang , Yohei Matsuzaki and Jeffrey A Whitsett BMC Genomics 2007, 8:455, Product: Pathway Studio |
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Vascular microarray profiling in two models of hypertension identifies caveolin-1, Rgs2 and Rgs5 as antihypertensive targets. Grayson TH, Ohms SJ, Brackenbury TD, Meaney KR, Peng K, Pittelkow YE, Wilson SR, Sandow SL, Hill CE. BMC Genomics. 2007 Nov 7;8:404., Product: Pathway Studio |
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Dexamethasone sensitizes the neonatal intestine to fructose-induction of GLUT5 transport function Veronique Douard, Xue-Lin Cui, Patricia Soteropoulos, and Ronaldo P. Ferraris Endocrinology, Oct 2007; 10.1210/en.2007-0906, Product: PathwayAssist |
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Genomic Changes in Regenerated Porcine Coronary Arterial Endothelial Cells Mary Y.K. Lee, Hung-Fat Tse, Chung-Wah Siu, Shu-Guang Zhu, Ricky Y.K. Man, and Paul M. Vanhoutte Arterioscler. Thromb. Vasc. Biol., Nov 2007; 27: 2443 - 2449, Product: PathwayAssist |
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Exposure to Arsenic at Levels Found in U.S. Drinking Water Modifies Expression in the Mouse Lung Angeline S. Andrew, Viviane Bernardo, Linda A. Warnke, Jennifer C. Davey, Thomas Hampton, Rebecca A. Mason, Jessica E.Thorpe, Michael A. Ihnat, and Joshua W. Hamilton Toxicol. Sci., Nov 2007; 100: 75 - 87, Product: Pathway Studio |
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Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes Tracy M Clement, Matthew D Anway, Mehmet Uzumcu, and Michael K Skinner Reproduction, Sep 2007; 134: 455 - 472, Product: PathwayAssist |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (2007) 7, 222 256, Product: PathwayAssist |
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Transcriptome teleonomy and scavenger lipidomics of albumin and alpha 1-acid glycoproteins: contextual genome-wide ontology enrichment as evidence for the epigenetic code? Pauli Ojala, , Sami Kilpinen, Lotta Arola, Petri Trnen, Elmar Bucher, Kalle Ojala, Kristiina Iljin, Mari Peltonen, Rolf Skotheim, Kristine Kleivi, Martti Tolvanen, Reija Autio, Pentti Somerharju, Olli Kallioniemi and Saara Laitinen Physics of Lipids, 149, p.S86-S86, Sep 2007, Product: Pathway Studio |
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Profiling Studies in Ovarian Cancer: A Review Rudolf S. N. Fehrmann, Xiang-yi Li, Ate G. J. van der Zee, Steven de Jong, Gerard J. te Meerman, Elisabeth G. E. de Vries, and Anne P. G. Crijns Oncologist, Aug 2007; 12: 960 - 966, Product: PathwayAssist |
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Big Results from Small Samples: Evaluation of Amplification Protocols for Gene Expression Profiling Agnes Viale, Juan Li, Jay Tiesman, Susan Hester, Aldo Massimi, Chandi Griffin, George Grills, Greg Khitrov, Kathryn Lilley, Kevin Knudtson, Bill Ward, Karl Kornacker, Chin-yi Chu, Herbert Auer, and Andrew I. Brooks Journal of Biomolecular Techniques, Product: PathwayAssist |
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Early gene expression profiles during intraoperative myocardial ischemia-reperfusion in cardiac surgery Sara Arab, Igor E. Konstantinov, Cathy Boscarino, Eva Cukerman, Alessandro Mori, Jia Li, Peter P. Liu, Andrew N. Redington, and John G. Coles J. Thorac. Cardiovasc. Surg., Jul 2007; 134: 74 - 81., Product: PathwayAssist |
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Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins A Budhu, Y Chen, J.W. Kim, M Forgues, K Valerie, C.C. Harris, and X.W. Wang Carcinogenesis, Product: PathwayAssist |
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Transcriptional network governing the angiogenic switch in human pancreatic cancer Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, Hauser K, Hahnfeldt P, Hlatky L, Debus J, Peters JM, Friess H, Folkman J, Huber PE. Proc Natl Acad Sci U S A. 2007 Jul 24, Product: Pathway Studio |
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Exenatide blocks JAK1-STAT1 in pancreatic beta cells Couto FM, Minn AH, Pise-Masison CA, Radonovich M, Brady JN, Hanson M, Fernandez LA, Wang P, Kendziorski C, Shalev A Metabolism. 2007 Jul;56(7):915-8, Product: Pathway Studio |
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Neutrophils: the forgotten cell in JIA disease pathogenesis James N Jarvis, Kaiyu Jiang, Howard R Petty, and Michael Centola Pediatr Rheumatol Online J. 2007; 5: 13., Product: Pathway Studio |
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Use of predictive gene expression signature from advanced-stage serous papillary ovarian cancer to identify biologically relevant molecular targets for chemoresponse L. Ozbun, T. Bonome, M. Radonovich, C. Pise-Masison, J. Brady, N. Caplen, M. Johnson, S. C. Mok, and M. J. Birrer ASCO Meeting Abstracts, Product: Pathway Studio |
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Tumor number and comparative micro-array analysis of tumor and adjacent non-tumor intestinal tissue after iron supplementation in ApcMin/+ mice James H. Swain, Adam M. Kresak, and Theresa P. Pretlow FASEB J, Apr 2007; 21: A384., Product: Pathway Studio |
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Global analysis of differentially expressed genes in androgen-independent prostate cancer Q Wei, M Li, X Fu, R Tang, Y Na, M Jiang, Y Li Prostate Cancer and Prostatic Diseases 10, 167 - 174, Product: Pathway Studio |
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Endothelial Cells\' Activation and Apoptosis Induced by a Subset of Antibodies against Human Cytomegalovirus: Relevance to the Pathogenesis of Atherosclerosis Lunardi C, Dolcino M, Peterlana D, Bason C, Navone R, Tamassia N, Tinazzi E, Beri R, Corrocher R, Puccetti A. PLoS ONE. 2007 May 30;2:e473, Product: Pathway Studio |
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Arthritis suppression by NADPH activation operates through an interferon- pathway Olofsson P, Nerstedt A, Hultqvist M, Nilsson EC, Andersson S, Bergelin A, Holmdahl R. BMC Biol. 2007 May 9;5:19, Product: Pathway Studio |
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C13-11 neovascularization in bland-white-garland syndrome A.A. Fokin, T.N. Masters, C. Gregory, F. Robicsek Interactive CardioVascular and Thoracic Surgery, 6: S1 - S172, Product: Pathway Studio |
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Gene expression profiling of human primary astrocytes exposed to manganese chloride indicates selective effects on several functions of the cells Amitabha Sengupta, Sarah M. Mense, Changgui Lana, Mei Zhou, Rory E. Mauro, Lisa Kellerman, Galina Bentsman, David J. Volsky, Elan D. Louis, Joseph H. Graziano and Li Zhang Neurotoxicology, 28 (3), p.478-489, May 2007, Product: Pathway Studio |
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Identification of human cell responses to benzene and benzene metabolites Bruce Gillis, Igor M. Gavin, Zarema Arbieva, Stephen T. King, Sundararajan Jayaraman, Bellur S. Prabhakar Genomics, Product: Pathway Studio, ResNet |
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Gap junction and purinergic P2 receptor proteins as a functional unit: insights from transcriptomics. Iacobas DA, Suadicani SO, Iacobas S, Chrisman C, Cohen MA, Spray DC, Scemes E. J Membr Biol. 2007 Jun;217(1-3):83-91, Product: Pathway Studio |
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Molecular networks in microarray analysis. Sivachenko AY, Yuryev A, Daraselia N, Mazo I. J Bioinform Comput Biol., Product: Pathway Studio, Topic: Gene expression analysis |
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Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs Adrian E. Platts, David J. Dix, Hector E. Chemes, Kary E. Thompson, Robert Goodrich, John C. Rockett, Vanesa Y. Rawe, Silvina Quintana, Michael P. Diamond, Lillian F. Strader, and Stephen A. Krawetz Hum. Mol. Genet., Apr 2007; 16: 763 - 773., Product: Pathway Studio |
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Glycerol kinase deficiency alters expression of genes involved in lipid metabolism, carbohydrate metabolism, and insulin signaling Rahib L, Maclennan NK, Horvath S, Liao JC, Dipple KM. Eur J Hum Genet. 2007 Apr 4, Product: Pathway Studio |
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Expression changes in mouse brains following nicotine-induced seizures; the modulation of transcription factor networks Merav Kedmi and Avi Orr-Urtreger Physiol Genomics, Apr 2007; 10.1152/physiolgenomics.00288.2006, Product: Pathway Studio |
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Highly purified CD38+ and CD38- sub-clones derived from the same chronic lymphocytic leukemia patient have distinct gene expression signatures despite their monoclonal origin C Pepper, R Ward, T T Lin, P Brennan, J Starczynski, M Musson, C Rowntree, P Bentley, K Mills, G Pratt, C Fegan Leukemia 21, 687 - 696 (01 Apr 2007), Product: Pathway Studio |
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Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation Peter G. Fuhrken, Chi Chen, William M. Millera, and Eleftherios T. Papoutsakis Experimental Hematology,V.35(3):476-489.e23, Product: Pathway Studio |
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Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis Eun Sung Park, Ju-Seog Lee, Hyun Goo Woo, Fenghuang Zhan, Joanna H. Shih, John D. Shaughnessy, Jr., and J. Frederic Mushinski PLoS ONE. 2007; 2(1): e145, Product: Pathway Studio |
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Gene Alterations Identified by Expression Profiling in Tumor-Associated Endothelial Cells from Invasive Ovarian Carcinoma Chunhua Lu, Tomas Bonome, Yang Li, Aparna A. Kamat, Liz Y. Han, Rosemarie Schmandt, Robert L. Coleman, David M. Gershenson, Robert B. Jaffe, Michael J. Birrer, and Anil K. Sood Cancer Res., Feb 2007; 67: 1757 - 1768, Product: PathwayAssist |
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The microglial gene regulatory network activated by interferon-gamma Moran, L.B.,Duke, D.C.,Graeber, M.B. Journal of Neuroimmunology, Feb 2007, Product: Pathway Studio |
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Ventral Tegmental Transcriptome Response to Intermittent Nicotine Treatment and Withdrawal in BALB/cJ, C57BL/6ByJ,and Quasi-Congenic RQI Mice Csaba Vadasz, Mariko Saito, Danielle O Brien,Jiri Zavadil, Grant Morahan, Goutam Chakraborty, Ray Wang Neurochem Res (2007) 32:457 480, Product: Pathway Studio |
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Interplay of Genes Regulated by Estrogen and Diindolylmethane in Breast Cancer Cell Lines Laura Mulvey, Alamelu Chandrasekaran, Kai Liu, Sarah Lombardi, Xue-Ping Wang, Karen J Auborn, and Leslie Goodwin Mol Med. 2007 Jan Feb; 13(1-2): 69 78, Product: Pathway Studio |
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Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation Siriluck Ponsuksili, Eduard Murani, Christina Walz, Manfred Schwerin, and Klaus Wimmers Physiol Genomics, Jan 2007; 10.1152/physiolgenomics.00178.2006, Product: PathwayAssist |
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A cassette system to study ES cell differentiation by inducible RNA interference Daniel Wegmller, Ines Raineri, Brigitte Gross, Edward J. Oakeley, and Christoph Moroni Stem Cells, Jan 2007; 10.1634/stemcells.2006-0106., Product: Pathway Studio |
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Bioinformatics analysis of the early inflammatory response in a rat thermal injury model Eric Yang, Timothy Maguire, Martin L Yarmush, Francois Berthiaume, and Ioannis P Androulakis BMC Bioinformatics. 2007; 8: 10, Product: Pathway Studio |
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Time-Dependent Rescue of Gene Expression by Androgens in the Mouse Proximal Caput Epididymidis-1 Cell Line after Androgen Withdrawal. Shayesta Seenundun and Bernard Robaire Endocrinology Vol. 148, No. 1 173-188, Product: Pathway Studio |
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Phenotypic and global gene expression profile changes between low passage and high passage MIN-6 cells Lorraine O Driscoll, Patrick Gammell, Eadaoin McKiernan, Eoin Ryan, Per Bendix Jeppesen, Sweta Rani, and Martin Clynes J. Endocrinol., Dec 2006; 191: 665 - 676, Product: PathwayAssist |
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Systems Analysis Of Pasteurella Multocida Response To Sub-Minimum Inhibitory Concentrations Of Antibiotics Bindu Nanduri, Mark L Lawrence,Shane C Burgess Mississippi Academy Of Sciences, Product: Pathway Studio |
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Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression Fernando O. Martinez, Siamon Gordon, Massimo Locati, and Alberto Mantovani J. Immunol., Nov 2006; 177: 7303 - 7311, Product: Pathway Studio |
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Peroxisome Proliferator-Activated Receptor Is Highly Expressed in Pancreatic Cancer and Is Associated With Shorter Overall Survival Times Glen Kristiansen, Juliane Jacob, Ann-Christin Buckendahl, Robert Grtzmann, Ingo Alldinger, Bence Sipos, Gnter Klppel, Marcus Bahra, Jan M. Langrehr, Peter Neuhaus, Manfred Dietel, and Christian Pilarsky Clin. Cancer Res., Nov 2006; 12: 6444 - 6451., Product: PathwayAssist |
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Essential role of Jun family transcription factors in PU.1 knockdown induced leukemic stem cells Ulrich Steidl, Frank Rosenbauer, Roel G W Verhaak, Xuesong Gu, Alexander Ebralidze, Hasan H Otu, Steffen Klippel, Christian Steidl, Ingmar Bruns, Daniel B Costa, Katharina Wagner, Manuel Aivado, Guido Kobbe, Peter J M Valk, Emmanuelle Passegu, Towia A Libermann, Ruud Delwel, Daniel G Tenen Nature Genetics 38, 1269 - 1277 (01 Nov 2006), Product: Pathway Studio |
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Molecular Network and Chromosomal Clustering of Genes Involved in Synaptic Plasticity in the Hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem, Product: Pathway Studio |
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Time dependent rescue of gene expression by androgens in the mouse proximal caput epididymidis (PC-1) cell line after androgen withdrawal Shayesta Seenundun and Bernard Robaire Endocrinology, Product: Pathway Studio |
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Characterization of differential gene expression profiles in diabetic embryopathy using DNA microarray analysis. Reece EA, Ji I, Wu YK, Zhao Z. Am J Obstet Gynecol. 2006 Oct;195(4):1075-80., Product: Pathway Studio |
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Identification of molecular markers and signaling pathway in endometrial cancer in Hong Kong Chinese women by genome-wide gene expression profiling Y F Wong, T H Cheung, K W K Lo, S F Yim, N S S Siu, S C S Chan, T W F Ho, K W Y Wong, M Y Yu, V W Wang, C Li, G J Gardner, T Bonome, W B Johnson, D I Smith, T K H Chung, M J Birrer Oncogene. 2006 Oct 16, Product: Pathway Studio |
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Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach Z A Rodd, B A Bertsch, W N Strother, H Le-Niculescu, Y Balaraman, E Hayden, R E Jerome, L Lumeng, J I Nurnberger, H J Edenberg, W J McBride, A B Niculescu The Pharmacogenomics Journal (10 Oct 2006), Product: Pathway Studio |
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Exercise affects the gene expression profiles of human white blood cells Buettner P, Mosig S, Lechtermann A, Funke H, Mooren FC. J Appl Physiol., Product: PathwayAssist |
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Cluster-based network model for time-course gene expression data Inoue LY, Neira M, Nelson C, Gleave M, Etzioni R. Biostatistics, Product: Pathway Studio |
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Agonist and Antagonist of Retinoic Acid Receptors Cause Similar Changes in Gene Expression and Induce Senescence-like Growth Arrest in MCF-7 Breast Carcinoma Cells Yuhong Chen, Milos Dokmanovic, Wilfred D. Stein, Robert J. Ardecky, and Igor B. Roninson Cancer Res., Sep 2006; 66: 8749 - 8761, Product: PathwayAssist |
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Respiratory Epithelial Gene Expression in Patients with Mild and Severe Cystic Fibrosis Lung Disease Jerry M. Wright, Christian A. Merlo, Jeffrey B. Reynolds, Pamela L. Zeitlin, Joe G. N. Garcia, William B. Guggino, and Michael P. Boyle Am. J. Respir. Cell Mol. Biol., Sep 2006; 35: 327 - 336., Product: Pathway Studio |
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Evidence for chronic, peripheral activation of neutrophils in polyarticular juvenile rheumatoid arthritis. Jarvis JN, Petty HR, Tang Y, Frank MB, Tessier PA, Dozmorov I, Jiang K, Kindzelski A, Chen Y, Cadwell C, Turner M, Szodoray P, McGhee JL, Centola M. Arthritis Res Ther. 2006; 8(5): R154, Product: Pathway Studio |
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Physiologic and Genomic Analyses of Nutrition-Ethanol Interactions During Gestation: Implications for Fetal Ethanol Toxicity Kartik Shankar, Mats Hidestrand, Xiaoli Liu, Rijin Xiao, Charles M. Skinner, Frank A. Simmen, Thomas M. Badger, and Martin J. J. Ronis Experimental Biology and Medicine, Sep 2006; 231: 1379 - 1397., Product: PathwayAssist |
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Identification of Cell Cycle Regulatory and Inflammatory Genes As Predominant Targets of p38 Mitogen-Activated Protein Kinase in the Heart Olli Tenhunen, Jaana Rys, Mika Ilves, Ylermi Soini, Heikki Ruskoaho, and Hanna Leskinen Circ. Res., Sep 2006; 99: 485 - 493., Product: PathwayAssist |
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Expression Profiling Identifies Altered Expression of Genes That Contribute to the Inhibition of Transforming Growth Factor- Signaling in Ovarian Cancer Jan S. Sunde, Howard Donninger, Kongming Wu, Michael E. Johnson, Richard G. Pestell, G. Scott Rose, Samuel C. Mok, John Brady, Tomas Bonome, and Michael J. Birrer Cancer Res.; 66: 8404 - 8412., Product: PathwayAssist |
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Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn and Eric G Bremer BMC Bioinformatics 2006, 7:373, Product: Pathway Studio |
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Identification and pathway analysis of immediate hyperosmotic stress responsive molecular mechanisms in tilapia (Oreochromis mossambicus) gill Diego F. Fiola, Stephanie Y. Chana and Dietmar Kltz Comparative Biochemistry and Physiology Part D: Genomics and Proteomics V1(3):344-356, Product: Pathway Studio |
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Phenotype-Based Screening of Mechanistically Annotated Compounds in Combination with Gene Expression and Pathway Analysis Identifies Candidate Drug Targets in a Human Squamous Carcinoma Cell Model Mrten Frykns, Linda Rickardson, Malin Wickstrm, Sumeer Dhar, Henrik Lvborg, Joachim Gullbo, Peter Nygren, Mats G. Gustafsson, Anders Isaksson, and Rolf Larsson J Biomol Screen., 11: 457 - 468, Product: PathwayAssist |
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The Microarray Data Analysis Process: From Raw Data to Biological Significance Olson, N.E. NeuroRX, Product: Pathway Studio |
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Stat3 Is Required for Cytoprotection of the Respiratory Epithelium during Adenoviral Infection Yohei Matsuzaki, Yan Xu, Machiko Ikegami, Valrie Besnard, Kwon-Sik Park, William M. Hull, Susan E. Wert and Jeffrey A. Whitsett2 The Journal of Immunology, 2006, 177: 527-537., Product: PathwayAssist |
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Celecoxib Treatment Alters the Gene Expression Profile of Normal Colonic Mucosa Oleg K. Glebov, Luz M. Rodriguez, Patrick Lynch, Sherri Patterson, Henry Lynch, Kenneth Nakahara, Jean Jenkins, Janet Cliatt, Casey-Jo Humbyrd, John DeNobile, Peter Soballe, Steven Gallinger, Aby Buchbinder, Gary Gordon, Ernest Hawk, and Ilan R. Kirsch Cancer Epidemiol. Biomarkers Prev., Jul 2006; 15: 1382 - 1391., Product: PathwayAssist, MedScan |
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Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus Chang Sin Park, Ruomu Gong, Joshua Stuart, and Shao-Jun Tang J. Biol. Chem., Jul 2006; 10.1074/jbc.M605876200., Product: PathwayAssist |
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Characterization of cell-type specific profiles in tissues and isolated cells from squamous cell carcinomas of the lung Lesleyann Hawthorn, Leighton Stein, Jenniffer Panzarella, Gregory M. Loewen and Heinz Baumann Lung Cancer, 04, 2006, Product: Pathway Studio |
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The Common Insecticides Cyfluthrin and Chlorpyrifos Alter the Expression of a Subset of Genes with Diverse Functions in Primary Human Astrocytes Sarah M. Mense, Amitabha Sengupta, Changgui Lan, Mei Zhou, Galina Bentsman, David J. Volsky, Robin M. Whyatt, Frederica P. Perera, and Li Zhang Toxicol. Sci., Jun 2006, Product: PathwayAssist |
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Signatures of human regulatory T cells: an encounter with old friends and new players. Pfoertner S, Jeron A, Probst-Kepper M, Guzman CA, Hansen W, Westendorf AM, Toepfer T, Schrader AJ, Franzke A, Buer J, Geffers R Genome Biol. 2006 Jun 12;7(7):, Product: Pathway Studio |
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Parallel analysis of transcript and translation profiles: identification of metastasis-related signal pathways differentially regulated by drug and genetic modifications Yang H, Yu LR, Yi M, Lucas DA, Lukes L, Lancaster M, Chan KC, Issaq HJ, Stephens RM, Conrads TP, Veenstra TD, Hunter KW. J Proteome Res. 2006 July 7; 5(7): 1555 1567., Product: Pathway Studio |
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Mechanisms and Effects of Loss of Human Leukocyte Antigen Class II Expression in Immune-Privileged Site-Associated B-Cell Lymphoma Marije Booman, Jenny Douwes, Annuska M. Glas, Sietske A. Riemersma, Ekaterina S. Jordanova, Klaas Kok, Andreas Rosenwald, Daphne de Jong, Ed Schuuring, and Philip M. Kluin Clin. Cancer Res., May 2006; 12: 2698 - 2705, Product: PathwayAssist |
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DNA microarray analysis of striatal gene expression in symptomatic transgenic Huntington\'s mice (R6/2) reveals... Crocker, S.F. Costain, W.J. Robertson, H.A. Brain Research, May 2006, Product: Pathway Studio |
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cis-Regulatory sequences of the genes involved in apoptosis, cell growth, and proliferation may provide a target for some of the effects of acute ethanol exposure Uddin, R.K. Singh, S.M. Brain Research, May 2006, Product: Pathway Studio |
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Gene expression alterations in brains of mice infected with three strains of scrapie. Skinner PJ, Abbassi H, Chesebro B, Race RE, Reilly C, Haase AT. BMC Genomics. 2006; 7: 114., Product: Pathway Studio |
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Transcriptional Signatures of Cellular Plasticity in Mice Lacking the {alpha}1 Subunit of GABA-A Receptors Igor Ponomarev, Rajani Maiya, Mark T. Harnett, Gwen L. Schafer, Andrey E. Ryabinin, Yuri A. Blednov, Hitoshi Morikawa, Stephen L. Boehm, II, Gregg E. Homanics, Ari Berman, Kerrie H. Lodowski, Susan E. Bergeson, and R. Adron Harris J. Neurosci., May 2006; 26: 5673 - 5683, Product: PathwayAssist |
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Functional Genomic Responses to Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and CFTR508 in the Lung Xu Y, Liu C, Clark JC, Whitsett JA. J Biol Chem. 2006 Apr 21;281(16):11279-11291, Product: PathwayAssist |
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Respiratory Epithelial Gene Expression in Cystic Fibrosis Patients with Mild and Severe Lung Disease. Wright JM, Merlo CA, Reynolds JB, Zeitlin PL, Garcia JG, Guggino WB, Boyle MP. Am J Respir Cell Mol Biol. 2006 Apr 13, Product: PathwayAssist |
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Gene Expression Profiling of Acute Liver Stress During Living Donor Liver Transplantation Borozan, I; Chen, L; Sun, J; Tannis, L.-L; Guindi, M; Rotstein, OD; Heathcote, J; Edwards, AM; Grant, D; McGilvray, ID American Journal of Transplantation, 6(4):806-824, 2006, Product: Pathway Studio |
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A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis Szodoray P, Alex P, Frank MB, Turner M, Turner S, Knowlton N, Cadwell C, Dozmorov I, Tang Y, Wilson PC, Jonsson R, Centola M. Rheumatology (Oxford). 2006 Apr 25;, Product: PathwayAssist |
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Gingival epithelial cells heterozygous for Toll-like receptor 4 polymorphisms Asp299Gly and Thr399ile are hypo-responsive to Porphyromonas gingivalis Kinane DF, Shiba H, Stathopoulou PG, Zhao H, Lappin DF, Singh A, Eskan MA, Beckers S, Waigel S, Alpert B, Knudsen TB. Genes and Immunity (2006) 7,, Product: Pathway Studio |
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A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells Ju-Seog Lee, Jeonghoon Heo, Louis Libbrecht, In-Sun Chu, Pal Kaposi-Novak, Diego F Calvisi, Arsen Mikaelyan, Lewis R Roberts, Anthony J Demetris, Zongtang Sun, Frederik Nevens, Tania Roskams & Snorri S Thorgeirsson Nature Medicine 12, 410 - 416 (2006), Product: Pathway Studio |
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Identification of novel prognostic subtype of hepatocellular carcinoma derived from hepatic stem cells by comparative functional genomic approach. Ju-Seog Lee, Jeonghoon Heo, Louis Libbrecht, In-Sun Chu, Pal Kaposi-Novak, Diego F. Calvisi, Arsen Mikaelyan, Lewis R. Roberts, Anthony J. Demetris, Zongtang Sun, Frederik Nevens, Tania Roskams, and Snorri S. Thorgeirsson ACR Meeting Abstracts, 2006: 1338 - 1339., Product: PathwayAssist |
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Global gene expression profiling of mucinous ovarian tumors and cystadenomas identifies genes of clinicopathologic importance Fred W. A. Wamunyokoli, Tomas Bonome, Ji-Young Lee, Colleen M. Feltmate, William R. Welch, Mike Radonovich, Cindy Pise-Masison, John Brady, Ke Hao, Ross S. Berkowitz, Samuel Mok, and Michael J. Birrer AACR Meeting Abstracts, 2006: 1057 - 1058, Product: PathwayAssist |
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Expression profiling of peripheral blood cells for early detection of breast cancer Jrgen M. Aare, Torbjrn Lindahl, Solve Sb, Per Skaane, Simen Myhre, Turid Reiersen, Anders Lnneborg, Anne-Lise Brresen-Dale, and Praveen Sharma AACR Meeting Abstracts,2006: 29 - 30., Product: PathwayAssist |
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Variants in the ATM-BRCA2-CHEK2 axis predispose to chronic lymphocytic leukaemia Rudd MF, Sellick GS, Webb EL, Catovsky D, Houlston RS. Blood. 2006 Mar 30, Product: PathwayAssist |
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Gene Expression Arrays in Juvenile Rheumatoid Arthritis: Will the Blind Men Finally See the Elephant? Jarvis, J.N. Current Problems in Pediatric and Adolescent Health Care, Mar 2006, Product: Pathway Studio |
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Activation of IFN pathways and plasmacytoid dendritic cell recruitment in target organs of primary Sjgren s syndrome Gottenberg JE, Cagnard N, Lucchesi C, Letourneur F, Mistou S, Lazure T, Jacques S, Ba N, Ittah M, Lepajolec C, Labetoulle M, Ardizzone M, Sibilia J, Fournier C, Chiocchia G, Mariette X. Proc Natl Acad Sci U S A. 2006 Feb 13, Product: PathwayAssist |
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Gene Expression Profiling Reveals the Profound Up-regulation of Hypoxia-Responsive Genes in Primary Human Astrocytes S. M Mense, A. Sengupta, M. Zhou, C. Lan, G. Bentsman, D. J Volsky, and L. Zhang Physiol. Genomics (February 28, 2006)., Product: PathwayAssist |
| A Pathway Analysis of Poly (I:C)-Induced Global Gene Expression Change in Human Peripheral Blood Monon |