Microarrays

Gene selection is of vital importance in molecular classification of cancer using high-dimensional gene expression data. Because of the distinct characteristics inherent to specific cancerous gene expression profiles, developing flexible and robust feature selection methods is extremely crucial. We investigated the properties of one feature selection approach proposed in our...

Gene selection is of vital importance in molecular classification of cancer using high-dimensional gene expression data. Because of the distinct characteristics inherent to specific cancerous gene expression profiles, developing flexible and robust feature selection methods is extremely crucial. We investigated the properties of one feature selection approach proposed in our...

Microarrays are becoming a widely used tool to study gene expression evolution. A recent paper by Wang and Rekaya describes a comprehensive study of gene expression evolution by microarray. The work provides a perspective to study gene expression evolution in terms of functional enrichment and promoter conservation. It was found...

This study aimed at discriminating carcinogens on the basis of hepatic transcript profiling in the rats administrated with a variety of carcinogens and non-carcinogens. We conducted 28-day toxicity tests in male F344 rats with 47 carcinogens and 26 non- carcinogens, and then investigated periodically the hepatic gene expression profiles using...

Microarray measurements of mRNA abundances is a standard tool for evaluation of transcriptional activity in functional genomics. The methodology underlying these measurements assumes existence of a direct link between transcription levels, that is, gene-specific mRNA copy numbers present in the cell, and transcription rates, that is, the numbers of gene-specific...

Laura Kennedy1, J. Keith Vass1, D. Ross Haggart1, Steve Moore1, Michael E. Burczynski2, Dan Crowther1 and Gino Miele1 1Translational Medicine Research Collaboration Laboratory, Sir James Black Centre, University of Dundee, Dundee, DD1 5EH, U.K. 2Biomarker Laboratory, Wyeth Research, Collegeville, U.S.A. Abstract Peripheral blood as a surrogate tissue...

Li-Xuan Qin Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, U.S.A. Abstract Background: MicroRNAs are believed to play an important role in gene expression regulation. They have been shown to be involved in cell cycle regulation and cancer. MicroRNA expression profiling became...

Amy G. Clark, Katherine M. Mackin and Mary H. Foster Departments of Medicine and Research Service, Duke University and Durham Veterans Affairs Medical Centers, Durham, North Carolina, U.S.A. Abstract Background: Anergy is a key mechanism controlling expression of autoreactive B cells and a major site for failed...

Owen Z. Woody, Andrew C. Doxey and Brendan J. McConkey Department of Biology, University of Waterloo, Waterloo, Ontario Canada Abstract Classical studies of the evolution of gene function have predominantly focused on mutations within protein coding regions. With the advent of microarrays, however, it has become possible...

Salla Suomi1,5, Hanna Taipaleenmäki2,5, Anne Seppänen1, Tommi Ripatti3,4, Kalervo Väänänen1, Teuvo Hentunen1, Anna-Marja Säämänen2 and Tiina Laitala-Leinonen1 1Bone Biology Research Consortium, Department of Anatomy, 2Department of Medical Biochemistry and Molecular Biology, Institute of Biomedicine, University of Turku, FI-20520, Finland. 3Department of Molecular Medicine, National Public Health Institute...

Gino Boily1, Patrick Beaulieu1, Jasmine Healy1 and Daniel Sinnett1,2 1Division of Hematology-Oncology, Charles-Bruneau Cancer Center, Research Center, CHU Sainte-Justine, Montreal, Quebec, Canada. 2Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada. Abstract Accumulating genetic and functional evidence point to ETV6 as being the...

Gino Boily1, Patrick Beaulieu1, Jasmine Healy1 and Daniel Sinnett1,2 1Division of Hematology-Oncology, Charles-Bruneau Cancer Center, Research Center, CHU Sainte-Justine, Montreal, Quebec, Canada. 2Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada. Abstract Accumulating genetic and functional evidence point to ETV6 as being the...

Yingdong Zhao and Richard Simon Biometric Research Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, U.S.A. Abstract The explosion of available microarray data on human cancer increases the urgency for developing methods for effectively sharing this data among clinical cancer investigators. Lack of a smooth interface...

Liang-Hui Chu and Bor-Sen Chen Lab of Control and Systems Biology, National Tsing Hua University, Hsinchu, 300, Taiwan. Abstract Robustness is defined as the ability to uphold performance in face of perturbations and uncertainties, and sensitivity is a measure of the system deviations generated by perturbations to the...

Aimee L. Jackson*1, Mao Mao*1, Sumire Kobayashi1, Teresa Ward1, Matthew Biery1, Hongyue Dai1, Steven R. Bartz2 and Peter S. Linsley1 1Rosetta Inpharmatics LLC, a wholly-owned subsidiary of Merck and Co., Inc., Seattle, WA 98109. 2Sirna Therapeutics, a wholly-owned subsidiary of Merck and Co., Inc., San Francisco, CA ...

Aimee L. Jackson*1, Mao Mao*1, Sumire Kobayashi1, Teresa Ward1, Matthew Biery1, Hongyue Dai1, Steven R. Bartz2 and Peter S. Linsley1 1Rosetta Inpharmatics LLC, a wholly-owned subsidiary of Merck and Co., Inc., Seattle, WA 98109. 2Sirna Therapeutics, a wholly-owned subsidiary of Merck and Co., Inc., San Francisco, CA ...

Hsiao-Wei Chen†,1,2, Hsuan-Cheng Huang†,3, Yi-Shing Lin4, King-Jen Chang5, Wen-Hung Kuo5, Hsiao-Lin Hwa6, Fon-Jou Hsieh1,6,9 and Hsueh-Fen Juan1,7,8,9 1Department of Life Science, National Taiwan University, Taipei 106, Taiwan. 2Institute of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan. 3Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan. 4Welgene Biotech....

Ali Kpatcha Kadanga, Christine Leroux, Muriel Bonnet, Stéphanie Chauvet, Bruno Meunier, Isabelle Cassar-Malek and Jean-François Hocquette INRA, UR1213, Unité de Recherches sur les Herbivores, Centre de Recherches de Clermont- Ferrand/Theix, F-63122 Saint Genès-Champanelle, France. Abstract This study was conducted with the aim of optimizing the experimental design of...

Masumi Akita1 and Keiko Fujita2 1Division of Morphological Science, Biomedical Research Center, Saitama Medical University, 38 Moroyama, Iruma-gun, Saitama 350-0495, Japan. 2Department of Anatomy, Saitama Medical University, 38 Moroyama, Iruma-gun, Saitama 350-0495, Japan. Abstract We examined angiogenesis-related gene expression profiles using collagen gel culture and a DNA chip....

A.-L. Boulesteix1, C. Strobl2, T. Augustin2 and M. Daumer1 1Sylvia Lawry Centre for MS Research (SLC), Hohenlindenerstr. 1, 81677 Munich, Germany. 2Department of Statistics, University of Munich (LMU), Ludwigstr. 33, 80539 Munich, Germany. Abstract For the last eight years, microarray-based class prediction has been the subject...

Akihiro Hirakawa1, Yasunori Sato2, Chikuma Hamada3 and Isao Yoshimura3 1Genetics Division, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan. 2Department of Biostatistics, Harvard School of Public Health, Boston, U.S.A. 3Faculty of Engineering, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan. Abstract Choosing an appropriate statistic and precisely evaluating...

Hongmei Jiang1 and R.W. Doerge2 1Department of Statistics, Northwestern University, 2006 Sheridan Road, Evanston, IL 60208 U.S.A. 2Department of Statistics, Purdue University, 250 N. University Street, West Lafayette, IN 47907 U.S.A. Abstract Whole genome microarray investigations (e.g. differential expression, differential methylation, ChIP-Chip) provide opportunities to test...

Doris M. Benbrook1,2, Stan Lightfoot3, James Ranger-Moore4, Tongzu Liu1, Shylet Chengedza2, William L. Berry5 and Igor Dozmorov6 1Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK. 2Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK. 3Department...

Akihiro Hirakawa1, Yasunori Sato1, Takashi Sozu2, Chikuma Hamada3, Isao Yoshimura3 1Genetics Division, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan. 2The Center for Advanced Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan. 3Faculty of Engineering, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan. Abstract The recent...

Ting Gong1, Jianhua Xuan1, Chen Wang1, Huai Li2, Eric Hoffman3, Robert Clarke4 and Yue Wang1 1Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, U.S.A. 2Bioinformatics Unit, Research Resources Branch, National Institute on Aging, NIH, Baltimore, MD...

Hyman M. Schipper1,2,3,4, Olivier C. Maes3,4,5, Howard M. Chertkow1,2,3,4 and Eugenia Wang51Department of Neurology and Neurosurgery and 2Department of Medicine (Geriatrics), McGill University, Montreal, Canada. 3Centre for Neurotranslational Research and 4Bloomfield Centre for Research in Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General...

Jun Xu1, Xutao Deng1,2, Victor Chan3, Nancy Kelley-Loughnane4, Brent W Harker5, Leming Shi6, Saber M. Hussain7, John M. Frazier7 and Charles Wang1,2 1Department of Medicine and Burns and Allen Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; 2David Geffen School of Medicine at UCLA, Los Angeles, CA 90048; 3Alion...

Alexandar Tzankov, Philip Went and Stephan Dirnhofer Department of Pathology, University Hospital Basel, Switzerland.Abstract: Diffuse large B-cell lymphomas (DLBCL) are the most common lymphoid malignancies, and encompass all malignant lymphomas characterized by large neoplastic cells and B-cell derivation. In the last decade, DLBCL has been subjected to intense clinical, phenotypic...

Shuangge Ma1 and Jian Huang2 1Department of Epidemiology and Public Health, Yale University, New Haven, CT, U.S.A. 2Departments of Statistics and Actuarial Science, University of Iowa, Iowa City, IA, U.S.A.Summary: Clinical covariates such as age, gender, tumor grade, and smoking history have been extensively used in prediction of disease occurrence...

Yu-Hsiang Chang, Yu-Chao Wang and Bor-Sen Chen Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan.Abstract: The trans-regulatory circuit is considered as the regulatory interactions between upstream regulatory genes and transcription factor binding site motifs or cis elements. And the cis-regulatory circuit...