Bioinformatics Vol. 18 no. 1 2002
Pages 207-208
© 2002 Oxford University Press
Applications Note |
Genesis: cluster analysis of microarray data
1 Institute of Biomedical Engineering, Graz
University of Technology, Krenngasse 37, 8010 Graz, Austria
2 The Institute for Genomic Research,
Rockville, MD 20850, USA
Received on June 23, 2000
; revised on August 21, 2000
; accepted on September 5, 2000
Summary: A versatile, platform independent and easy to use Java suite for large-scale gene expression analysis was developed. Genesis integrates various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines. The results of the clustering are transparent across all implemented methods and enable the analysis of the outcome of different algorithms and parameters. Additionally, mapping of gene expression data onto chromosomal sequences was implemented to enhance promoter analysis and investigation of transcriptional control mechanisms.
Availability: http://genome.tugraz.at
Contact: zlatko.trajanoski{at}tugraz.at
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  V. C. Banduseela, J. Ochala, Y.-W. Chen, H. Goransson, H. Norman, P. Radell, L. I. Eriksson, E. P. Hoffman, and L. Larsson Gene expression and muscle fiber function in a porcine ICU model Physiol Genomics, November 1, 2009; 39(3): 141 - 159. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Suo, Y. Jiang, B. Cowan, and J. Y.J. Wang Platelet-Derived Growth Factor C Is Upregulated in Human Uterine Fibroids and Regulates Uterine Smooth Muscle Cell Growth Biol Reprod, October 1, 2009; 81(4): 749 - 758. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. K. G. Kadegowda, M. Bionaz, L. S. Piperova, R. A. Erdman, and J. J. Loor Peroxisome proliferator-activated receptor-{gamma} activation and long-chain fatty acids alter lipogenic gene networks in bovine mammary epithelial cells to various extents J Dairy Sci, September 1, 2009; 92(9): 4276 - 4289. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Pesaresi, A. Hertle, M. Pribil, T. Kleine, R. Wagner, H. Strissel, A. Ihnatowicz, V. Bonardi, M. Scharfenberg, A. Schneider, et al. Arabidopsis STN7 Kinase Provides a Link between Short- and Long-Term Photosynthetic Acclimation PLANT CELL, August 1, 2009; 21(8): 2402 - 2423. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Reddy, S. Jia, R. Geoffrey, R. Lorier, M. Suchi, U. Broeckel, M. J. Hessner, and J. Verbsky An Autoinflammatory Disease Due to Homozygous Deletion of the IL1RN Locus N. Engl. J. Med., June 4, 2009; 360(23): 2438 - 2444. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Rojo, I. Gonzalez-Navarrete, R. Bragado, A. Dalmases, S. Menendez, M. Cortes-Sempere, C. Suarez, C. Oliva, S. Servitja, V. Rodriguez-Fanjul, et al. Mitogen-Activated Protein Kinase Phosphatase-1 in Human Breast Cancer Independently Predicts Prognosis and Is Repressed by Doxorubicin Clin. Cancer Res., May 15, 2009; 15(10): 3530 - 3539. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Mellberg, A. Dimberg, F. Bahram, M. Hayashi, E. Rennel, A. Ameur, J. O. Westholm, E. Larsson, P. Lindahl, M. J. Cross, et al. Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis FASEB J, May 1, 2009; 23(5): 1490 - 1502. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. X. Lu, A. Munitz, and M. E. Rothenberg MicroRNA-21 Is Up-Regulated in Allergic Airway Inflammation and Regulates IL-12p35 Expression J. Immunol., April 15, 2009; 182(8): 4994 - 5002. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. H. S. Richter, S. Plehm, A. Fasan, S. Rossler, R. Unland, I. M. Bennani-Baiti, M. Hotfilder, D. Lowel, I. von Luettichau, I. Mossbrugger, et al. EZH2 is a mediator of EWS/FLI1 driven tumor growth and metastasis blocking endothelial and neuro-ectodermal differentiation PNAS, March 31, 2009; 106(13): 5324 - 5329. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Camus, M. Tosolini, B. Mlecnik, F. Pages, A. Kirilovsky, A. Berger, A. Costes, G. Bindea, P. Charoentong, P. Bruneval, et al. Coordination of Intratumoral Immune Reaction and Human Colorectal Cancer Recurrence Cancer Res., March 15, 2009; 69(6): 2685 - 2693. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Pan, C. Kumar, S. Bohl, U. Klingmueller, and M. Mann Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions Mol. Cell. Proteomics, March 1, 2009; 8(3): 443 - 450. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W.-K. Chen, J. D. Swartz, L. J. Rush, and C. E. Alvarez Mapping DNA structural variation in dogs Genome Res., March 1, 2009; 19(3): 500 - 509. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. E. Cozen, M. T. Weirauch, K. S. Pollard, D. L. Bernick, J. M. Stuart, and T. M. Lowe Transcriptional Map of Respiratory Versatility in the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum J. Bacteriol., February 1, 2009; 191(3): 782 - 794. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. K. Cho, S. Geimer, and J. Meurer Cluster Analysis and Comparison of Various Chloroplast Transcriptomes and Genes in Arabidopsis thaliana DNA Res, February 1, 2009; 16(1): 31 - 44. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Mariappan, J. Winkler, S. Chen, H. Schulz, J. Hescheler, and A. Sachinidis Transcriptional profiling of CD31(+) cells isolated from murine embryonic stem cells. Genes Cells, February 1, 2009; 14(2): 243 - 260. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Hu, Y.-S. Su, and J. C. Lagarias A Light-Independent Allele of Phytochrome B Faithfully Recapitulates Photomorphogenic Transcriptional Networks Mol Plant, January 1, 2009; 2(1): 166 - 182. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Diaz-Riquelme, D. Lijavetzky, J. M. Martinez-Zapater, and M. J. Carmona Genome-Wide Analysis of MIKCC-Type MADS Box Genes in Grapevine Plant Physiology, January 1, 2009; 149(1): 354 - 369. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. L. Campbell, H. Christman, and J. C. Meeks DNA Microarray Comparisons of Plant Factor- and Nitrogen Deprivation-Induced Hormogonia Reveal Decision-Making Transcriptional Regulation Patterns in Nostoc punctiforme J. Bacteriol., November 15, 2008; 190(22): 7382 - 7391. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Gao, A. S. Barth, D. DiSilvestre, F. G. Akar, Y. Tian, A. Tanskanen, D. A. Kass, R. L. Winslow, and G. F. Tomaselli Key pathways associated with heart failure development revealed by gene networks correlated with cardiac remodeling Physiol Genomics, November 12, 2008; 35(3): 222 - 230. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Berg, M. Fliegauf, J. Burger, M. S. Staege, S. Liu, N. Martinez, O. Heidenreich, S. Burdach, T. Haferlach, M. H. Werner, et al. Transcriptional upregulation of p21/WAF/Cip1 in myeloid leukemic blasts expressing AML1-ETO Haematologica, November 1, 2008; 93(11): 1728 - 1733. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Argyris, P. Dahal, E. Hayashi, D. W. Still, and K. J. Bradford Genetic Variation for Lettuce Seed Thermoinhibition Is Associated with Temperature-Sensitive Expression of Abscisic Acid, Gibberellin, and Ethylene Biosynthesis, Metabolism, and Response Genes Plant Physiology, October 1, 2008; 148(2): 926 - 947. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. T. Yeung, B. B. Patel, X.-M. Li, S. H. Seeholzer, R. A. Coudry, H. S. Cooper, A. Bellacosa, B. M. Boman, T. Zhang, S. Litwin, et al. One-Hit Effects in Cancer: Altered Proteome of Morphologically Normal Colon Crypts in Familial Adenomatous Polyposis Cancer Res., September 15, 2008; 68(18): 7579 - 7586. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Hernandez-Novoa, L. Bishop, C. Logun, P. J. Munson, E. Elnekave, Z. G. Rangel, J. Barb, R. L. Danner, and J. A. Kovacs Immune responses to Pneumocystis murina are robust in healthy mice but largely absent in CD40 ligand-deficient mice J. Leukoc. Biol., August 1, 2008; 84(2): 420 - 430. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Aviel-Ronen, B. P. Coe, S. K. Lau, G. da Cunha Santos, C.-Q. Zhu, D. Strumpf, I. Jurisica, W. L. Lam, and M.-S. Tsao Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features PNAS, July 22, 2008; 105(29): 10155 - 10160. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Koyanagi, L. Y. Wong, K. Inagaki, O. V. Petrauskene, and D. Mochly-Rosen Alteration of gene expression during progression of hypertension-induced cardiac dysfunction in rats Am J Physiol Heart Circ Physiol, July 1, 2008; 295(1): H220 - H226. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J R Kerr, B Burke, R Petty, J Gough, D Fear, D L Mattey, J S Axford, A G Dalgleish, and D J Nutt Seven genomic subtypes of chronic fatigue syndrome/myalgic encephalomyelitis: a detailed analysis of gene networks and clinical phenotypes J. Clin. Pathol., June 1, 2008; 61(6): 730 - 739. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Verdoni, N. Aoyama, A. Ikeda, and S. Ikeda Effect of destrin mutations on the gene expression profile in vivo Physiol Genomics, June 1, 2008; 34(1): 9 - 21. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Haupl, M. Ostensen, A. Grutzkau, G.-R. Burmester, and P. M. Villiger Interaction between rheumatoid arthritis and pregnancy: correlation of molecular data with clinical disease activity measures Rheumatology, June 1, 2008; 47(suppl_3): iii19 - iii22. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. S. Gunasekera, L. N. Csonka, and O. Paliy Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses J. Bacteriol., May 15, 2008; 190(10): 3712 - 3720. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. G. Acevedo, M. Bieda, R. Green, and P. J. Farnham Analysis of the Mechanisms Mediating Tumor-Specific Changes in Gene Expression in Human Liver Tumors Cancer Res., April 15, 2008; 68(8): 2641 - 2651. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Graumann, N. C. Hubner, J. B. Kim, K. Ko, M. Moser, C. Kumar, J. Cox, H. Scholer, and M. Mann Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Proteome Quantitation of Mouse Embryonic Stem Cells to a Depth of 5,111 Proteins Mol. Cell. Proteomics, April 1, 2008; 7(4): 672 - 683. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. C. Martinez, K. Tanabe, C. Cras-Meneur, N. A. Abumrad, E. Bernal-Mizrachi, and M. A. Permutt Inhibition of Foxo1 Protects Pancreatic Islet {beta}-Cells Against Fatty Acid and Endoplasmic Reticulum Stress-Induced Apoptosis Diabetes, April 1, 2008; 57(4): 846 - 859. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Ruffel, S. Freixes, S. Balzergue, P. Tillard, C. Jeudy, M. L. Martin-Magniette, M. J. van der Merwe, K. Kakar, J. Gouzy, A. R. Fernie, et al. Systemic Signaling of the Plant Nitrogen Status Triggers Specific Transcriptome Responses Depending on the Nitrogen Source in Medicago truncatula Plant Physiology, April 1, 2008; 146(4): 2020 - 2035. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Martens, K. Vandepoele, and Y. Van de Peer Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species PNAS, March 4, 2008; 105(9): 3427 - 3432. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Bredhult, L. Sahlin, and M. Olovsson Gene expression analysis of human endometrial endothelial cells exposed to op'-DDT Mol. Hum. Reprod., February 1, 2008; 14(2): 97 - 106. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Wang, S. Jia, R. Geoffrey, R. Alemzadeh, S. Ghosh, and M. J. Hessner Identification of a Molecular Signature in Human Type 1 Diabetes Mellitus Using Serum and Functional Genomics J. Immunol., February 1, 2008; 180(3): 1929 - 1937. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Wen, J. A. Torres-Acosta, L. Pastushok, X. Lai, L. Pelzer, H. Wang, and W. Xiao Arabidopsis UEV1D Promotes Lysine-63-Linked Polyubiquitination and Is Involved in DNA Damage Response PLANT CELL, January 1, 2008; 20(1): 213 - 227. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Hansen, A. M. Westendorf, S. Reinwald, D. Bruder, S. Deppenmeier, L. Groebe, M. Probst-Kepper, A. D. Gruber, R. Geffers, and J. Buer Chronic Antigen Stimulation In Vivo Induces a Distinct Population of Antigen-Specific Foxp3 CD25 Regulatory T Cells J. Immunol., December 15, 2007; 179(12): 8059 - 8068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Shi, W. Zhou, and D. Xu Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analyzing their coexistence and related gene ontology Physiol Genomics, November 14, 2007; 31(3): 374 - 384. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. L. Toth, K. Varala, T. C. Newman, F. E. Miguez, S. K. Hutchison, D. A. Willoughby, J. F. Simons, M. Egholm, J. H. Hunt, M. E. Hudson, et al. Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality Science, October 19, 2007; 318(5849): 441 - 444. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Knoops, R. Haas, S. de Kemp, D. Majoor, A. Broeks, E. Eldering, J. P. de Boer, M. Verheij, C. van Ostrom, A. de Vries, et al. In vivo p53 response and immune reaction underlie highly effective low-dose radiotherapy in follicular lymphoma Blood, August 15, 2007; 110(4): 1116 - 1122. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Rodriguez, J. Mages, H. Dietrich, N. Wantia, H. Wagner, R. Lang, and T. Miethke MyD88-dependent changes in the pulmonary transcriptome after infection with Chlamydia pneumoniae Physiol Genomics, July 18, 2007; 30(2): 134 - 145. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Lu, X. He, and S. Zhong Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease Nucleic Acids Res., July 13, 2007; 35(suppl_2): W105 - W114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Adachi, C. Kumar, Y. Zhang, and M. Mann In-depth Analysis of the Adipocyte Proteome by Mass Spectrometry and Bioinformatics Mol. Cell. Proteomics, July 1, 2007; 6(7): 1257 - 1273. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Piriyapongsa, L. Marino-Ramirez, and I. K. Jordan Origin and Evolution of Human microRNAs From Transposable Elements Genetics, June 1, 2007; 176(2): 1323 - 1337. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. K. Mayer, M. Muehmer, J. Mages, K. Gueinzius, C. Hess, K. Heeg, R. Bals, R. Lang, and A. H. Dalpke Differential Recognition of TLR-Dependent Microbial Ligands in Human Bronchial Epithelial Cells J. Immunol., March 1, 2007; 178(5): 3134 - 3142. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Fardeau, G. Lelandais, A. Oldfield, H. Salin, S. Lemoine, M. Garcia, V. Tanty, S. Le Crom, C. Jacq, and F. Devaux The Central Role of PDR1 in the Foundation of Yeast Drug Resistance J. Biol. Chem., February 16, 2007; 282(7): 5063 - 5074. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Bellin, B. Schulz, T. R. Soerensen, F. Salamini, and K. Schneider Transcript profiles at different growth stages and tap-root zones identify correlated developmental and metabolic pathways of sugar beet J. Exp. Bot., February 1, 2007; 58(3): 699 - 715. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Glas, L. Knoops, L. Delahaye, M. J. Kersten, R. E. Kibbelaar, L. A. Wessels, R. van Laar, J. H. J.M. van Krieken, J. W. Baars, J. Raemaekers, et al. Gene-Expression and Immunohistochemical Study of Specific T-Cell Subsets and Accessory Cell Types in the Transformation and Prognosis of Follicular Lymphoma J. Clin. Oncol., February 1, 2007; 25(4): 390 - 398. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. B. Vos, N. A. Datson, K. F. Rabe, and P. S. Hiemstra Exploring host-pathogen interactions at the epithelial surface: application of transcriptomics in lung biology Am J Physiol Lung Cell Mol Physiol, February 1, 2007; 292(2): L367 - L377. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Beyhan, K. Bilecen, S. R. Salama, C. Casper-Lindley, and F. H. Yildiz Regulation of Rugosity and Biofilm Formation in Vibrio cholerae: Comparison of VpsT and VpsR Regulons and Epistasis Analysis of vpsT, vpsR, and hapR J. Bacteriol., January 15, 2007; 189(2): 388 - 402. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Diallo-Danebrock, E. Ting, O. Gluz, A. Herr, S. Mohrmann, H. Geddert, A. Rody, K.-L. Schaefer, S. E. Baldus, A. Hartmann, et al. Protein Expression Profiling in High-Risk Breast Cancer Patients Treated with High-Dose or Conventional Dose-Dense Chemotherapy Clin. Cancer Res., January 15, 2007; 13(2): 488 - 497. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. R. Nagy, B. Gyorffy, O. Galamb, B. Molnar, B. Nagy, and Z. Papp Use of Routinely Collected Amniotic Fluid for Whole-Genome Expression Analysis of Polygenic Disorders Clin. Chem., November 1, 2006; 52(11): 2013 - 2020. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Galon, A. Costes, F. Sanchez-Cabo, A. Kirilovsky, B. Mlecnik, C. Lagorce-Pages, M. Tosolini, M. Camus, A. Berger, P. Wind, et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science, September 29, 2006; 313(5795): 1960 - 1964. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Larochelle, S. Drouin, F. Robert, and B. Turcotte Oxidative Stress-Activated Zinc Cluster Protein Stb5 Has Dual Activator/Repressor Functions Required for Pentose Phosphate Pathway Regulation and NADPH Production. Mol. Cell. Biol., September 1, 2006; 26(17): 6690 - 6701. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Rainer, F. Sanchez-Cabo, G. Stocker, A. Sturn, and Z. Trajanoski CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W498 - W503. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Kote-Jarai, L. Matthews, A. Osorio, S. Shanley, I. Giddings, F. Moreews, I. Locke, D. G. Evans, D. Eccles, The Carrier Clinic Collaborators, et al. Accurate Prediction of BRCA1 and BRCA2 Heterozygous Genotype Using Expression Profiling after Induced DNA Damage. Clin. Cancer Res., July 1, 2006; 12(13): 3896 - 3901. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Handley, P. H. Dube, and V. L. Miller From the Cover: Histamine signaling through the H2 receptor in the Peyer's patch is important for controlling Yersinia enterocolitica infection PNAS, June 13, 2006; 103(24): 9268 - 9273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. D. Morin, E. Chang, A. Petrescu, N. Liao, M. Griffith, R. Kirkpatrick, Y. S. Butterfield, A. C. Young, J. Stott, S. Barber, et al. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling Genome Res., June 1, 2006; 16(6): 796 - 803. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Booman, J. Douwes, A. M. Glas, S. A. Riemersma, E. S. Jordanova, K. Kok, A. Rosenwald, D. de Jong, E. Schuuring, and P. M. Kluin Mechanisms and Effects of Loss of Human Leukocyte Antigen Class II Expression in Immune-Privileged Site-Associated B-Cell Lymphoma. Clin. Cancer Res., May 1, 2006; 12(9): 2698 - 2705. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E P Slater, S M Diehl, P Langer, B Samans, A Ramaswamy, A Zielke, and D K Bartsch Analysis by cDNA microarrays of gene expression patterns of human adrenocortical tumors. Eur. J. Endocrinol., April 1, 2006; 154(4): 587 - 598. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. A. Hollmann, T. Owens, J. Nalbantoglu, T. J. Hudson, and R. Sladek Constitutive Activation of Extracellular Signal-Regulated Kinase Predisposes Diffuse Large B-Cell Lymphoma Cell Lines to CD40-Mediated Cell Death. Cancer Res., April 1, 2006; 66(7): 3550 - 3557. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Hessner, B. Xiang, S. Jia, R. Geoffrey, S. Holmes, L. Meyer, S. Muheisen, and X. Wang Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms Physiol Genomics, March 13, 2006; 25(1): 166 - 178. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Klimmek, A. Sjodin, C. Noutsos, D. Leister, and S. Jansson Abundantly and Rarely Expressed Lhc Protein Genes Exhibit Distinct Regulation Patterns in Plants Plant Physiology, March 1, 2006; 140(3): 793 - 804. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. C. G. Weaver, M. J. Meaney, and M. Szyf Maternal care effects on the hippocampal transcriptome and anxiety-mediated behaviors in the offspring that are reversible in adulthood PNAS, February 28, 2006; 103(9): 3480 - 3485. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Hammer, J. Mages, H. Dietrich, A. Servatius, N. Howells, A. C.B. Cato, and R. Lang Dual specificity phosphatase 1 (DUSP1) regulates a subset of LPS-induced genes and protects mice from lethal endotoxin shock J. Exp. Med., January 23, 2006; 203(1): 15 - 20. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Combs, R. J. Nagel, M. Ares Jr., and S. W. Stevens Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis Mol. Cell. Biol., January 15, 2006; 26(2): 523 - 534. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Spence, B. M. Duggan, C. Eckhardt, M. McClelland, and D. Mercola Messenger RNAs under Differential Translational Control in Ki-ras-Transformed Cells Mol. Cancer Res., January 1, 2006; 4(1): 47 - 60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Pages, A. Berger, M. Camus, F. Sanchez-Cabo, A. Costes, R. Molidor, B. Mlecnik, A. Kirilovsky, M. Nilsson, D. Damotte, et al. Effector Memory T Cells, Early Metastasis, and Survival in Colorectal Cancer N. Engl. J. Med., December 22, 2005; 353(25): 2654 - 2666. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Helming, J. Bose, J. Ehrchen, S. Schiebe, T. Frahm, R. Geffers, M. Probst-Kepper, R. Balling, and A. Lengeling 1{alpha},25-dihydroxyvitamin D3 is a potent suppressor of interferon {gamma}-mediated macrophage activation Blood, December 15, 2005; 106(13): 4351 - 4358. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Dutu, S. Michiels, P. Fouret, F. Penault-Llorca, P. Validire, S. Benhamou, E. Taranchon, L. Morat, D. Grunenwald, T. Le Chevalier, et al. Differential expression of biomarkers in lung adenocarcinoma: a comparative study between smokers and never-smokers Ann. Onc., December 1, 2005; 16(12): 1906 - 1914. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Enver, S. Soneji, C. Joshi, J. Brown, F. Iborra, T. Orntoft, T. Thykjaer, E. Maltby, K. Smith, R. A. Dawud, et al. Cellular differentiation hierarchies in normal and culture-adapted human embryonic stem cells Hum. Mol. Genet., November 1, 2005; 14(21): 3129 - 3140. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. M. Berquin, Y. Min, R. Wu, H. Wu, and Y. Q. Chen Expression Signature of the Mouse Prostate J. Biol. Chem., October 28, 2005; 280(43): 36442 - 36451. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Fratelli, L. O. Goodwin, U. A. Orom, S. Lombardi, R. Tonelli, M. Mengozzi, and P. Ghezzi Gene expression profiling reveals a signaling role of glutathione in redox regulation PNAS, September 27, 2005; 102(39): 13998 - 14003. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Sparks, H. Xie, R. A. Koza, R. Mynatt, M. W. Hulver, G. A. Bray, and S. R. Smith A High-Fat Diet Coordinately Downregulates Genes Required for Mitochondrial Oxidative Phosphorylation in Skeletal Muscle Diabetes, July 1, 2005; 54(7): 1926 - 1933. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. J. Wild, A. Herr, C. Wissmann, R. Stoehr, A. Rosenthal, D. Zaak, R. Simon, R. Knuechel, C. Pilarsky, and A. Hartmann Gene Expression Profiling of Progressive Papillary Noninvasive Carcinomas of the Urinary Bladder Clin. Cancer Res., June 15, 2005; 11(12): 4415 - 4429. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hannemann, H. M. Oosterkamp, C. A.J. Bosch, A. Velds, L. F.A. Wessels, C. Loo, E. J. Rutgers, S. Rodenhuis, and M. J. van de Vijver Changes in Gene Expression Associated With Response to Neoadjuvant Chemotherapy in Breast Cancer J. Clin. Oncol., May 20, 2005; 23(15): 3331 - 3342. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. S. Barth, S. Merk, E. Arnoldi, L. Zwermann, P. Kloos, M. Gebauer, K. Steinmeyer, M. Bleich, S. Kaab, M. Hinterseer, et al. Reprogramming of the Human Atrial Transcriptome in Permanent Atrial Fibrillation: Expression of a Ventricular-Like Genomic Signature Circ. Res., May 13, 2005; 96(9): 1022 - 1029. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. J. Wisser, Q. Sun, S. H. Hulbert, S. Kresovich, and R. J. Nelson Identification and Characterization of Regions of the Rice Genome Associated With Broad-Spectrum, Quantitative Disease Resistance Genetics, April 1, 2005; 169(4): 2277 - 2293. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. G. Frye, S. Porwollik, F. Blackmer, P. Cheng, and M. McClelland Host Gene Expression Changes and DNA Amplification during Temperate Phage Induction J. Bacteriol., February 15, 2005; 187(4): 1485 - 1492. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Ludwig, J. Mages, C. Staib, M. H. Lehmann, R. Lang, and G. Sutter Role of Viral Factor E3L in Modified Vaccinia Virus Ankara Infection of Human HeLa Cells: Regulation of the Virus Life Cycle and Identification of Differentially Expressed Host Genes J. Virol., February 15, 2005; 79(4): 2584 - 2596. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Bolshakova, F. Azuaje, and Pád. Cunningham An integrated tool for microarray data clustering and cluster validity assessment Bioinformatics, February 15, 2005; 21(4): 451 - 455. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Ohsugi, C. Cras-Meneur, Y. Zhou, E. Bernal-Mizrachi, J. D. Johnson, D. S. Luciani, K. S. Polonsky, and M. A. Permutt Reduced Expression of the Insulin Receptor in Mouse Insulinoma (MIN6) Cells Reveals Multiple Roles of Insulin Signaling in Gene Expression, Proliferation, Insulin Content, and Secretion J. Biol. Chem., February 11, 2005; 280(6): 4992 - 5003. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Gyaneshwar, O. Paliy, J. McAuliffe, D. L. Popham, M. I. Jordan, and S. Kustu Sulfur and Nitrogen Limitation in Escherichia coli K-12: Specific Homeostatic Responses J. Bacteriol., February 1, 2005; 187(3): 1074 - 1090. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Glas, M. J. Kersten, L. J. M. J. Delahaye, A. T. Witteveen, R. E. Kibbelaar, A. Velds, L. F. A. Wessels, P. Joosten, R. M. Kerkhoven, R. Bernards, et al. Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment Blood, January 1, 2005; 105(1): 301 - 307. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. May, H. Hauser, and D. Wirth Transcriptional control of SV40 T-antigen expression allows a complete reversion of immortalization Nucleic Acids Res., October 14, 2004; 32(18): 5529 - 5538. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Kubis, R. Patel, J. Combe, J. Bedard, S. Kovacheva, K. Lilley, A. Biehl, D. Leister, G. Rios, C. Koncz, et al. Functional Specialization amongst the Arabidopsis Toc159 Family of Chloroplast Protein Import Receptors PLANT CELL, August 1, 2004; 16(8): 2059 - 2077. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Palyada, D. Threadgill, and A. Stintzi Iron Acquisition and Regulation in Campylobacter jejuni J. Bacteriol., July 15, 2004; 186(14): 4714 - 4729. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Almstrup, C. E. Hoei-Hansen, U. Wirkner, J. Blake, C. Schwager, W. Ansorge, J. E. Nielsen, N. E. Skakkebaek, E. R.-D. Meyts, and H. Leffers Embryonic Stem Cell-Like Features of Testicular Carcinoma in Situ Revealed by Genome-Wide Gene Expression Profiling Cancer Res., July 15, 2004; 64(14): 4736 - 4743. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Ohsugi, C. Cras-Meneur, Y. Zhou, W. Warren, E. Bernal-Mizrachi, and M. A. Permutt Glucose and Insulin Treatment of Insulinoma Cells Results in Transcriptional Regulation of a Common Set of Genes Diabetes, June 1, 2004; 53(6): 1496 - 1508. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Kote-Jarai, R. D. Williams, N. Cattini, M. Copeland, I. Giddings, R. Wooster, R. H. tePoele, P. Workman, B. Gusterson, J. Peacock, et al. Gene Expression Profiling after Radiation-Induced DNA Damage Is Strongly Predictive of BRCA1 Mutation Carrier Status Clin. Cancer Res., February 1, 2004; 10(3): 958 - 963. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Bruno, R. Hoffmann, F. McBlane, J. Brown, R. Gupta, C. Joshi, S. Pearson, T. Seidl, C. Heyworth, and T. Enver Molecular Signatures of Self-Renewal, Differentiation, and Lineage Choice in Multipotential Hemopoietic Progenitor Cells In Vitro Mol. Cell. Biol., January 15, 2004; 24(2): 741 - 756. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Weigelt, A. M. Glas, L. F. A. Wessels, A. T. Witteveen, J. L. Peterse, and L. J. van't Veer Gene expression profiles of primary breast tumors maintained in distant metastases PNAS, December 23, 2003; 100(26): 15901 - 15905. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Kutlu, A. K. Cardozo, M. I. Darville, M. Kruhoffer, N. Magnusson, T. Orntoft, and D. L. Eizirik Discovery of Gene Networks Regulating Cytokine-Induced Dysfunction and Apoptosis in Insulin-Producing INS-1 Cells Diabetes, November 1, 2003; 52(11): 2701 - 2719. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Xu, V. Olman, L. Wang, and Y. Xu EXCAVATOR: a computer program for efficiently mining gene expression data Nucleic Acids Res., October 1, 2003; 31(19): 5582 - 5589. [Abstract] [Full Text] [PDF]
|
|