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基因芯片技术资源
一. 生物芯片一般信息与公司网站 二. 文献 三. 基因表达数据库 四. 分析软件 五. 数据分析研究组 六. 其他 一. 生物芯片一般信息与公司网站： 概 观 联合基因 上海博星 陕西超群 工艺概述 南京益来 生物芯片网 生物芯片技术信息网 清华大学生物芯片研发中心 Clontech公司 Displaysystems公司 Genomesystems公司 Research Genetics公司 二. 文 献： http://linkage.rockefeller.edu/wli/microarray/ http://citeseer.nj.nec.com/cs 三. 基因表达数据库： GEO - by NCBI ASDB - Protein products and expression patterns of alternatively-spliced genes Axeldb - Gene expression in Xenopus BodyMap - Human and mouse gene expression data EpoDB - Genes expressed in vertebrate RBC FlyView - Drosophila development and genetics Gene Expression Database (GXD) - Mouse gene expression and genomics Kidney Development Database - Kidney development and gene expression MAGEST - Ascidian (Halocynthia roretzi) gene expression patterns Mouse Atlas and Gene Expression Database - Spatially-mapped gene expression data PEDB - Normal and aberrant prostate gene expression Tooth Development Database - Gene expression in dental tissue TRIPLES - TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces - Gene expression in Xenopus ARRAYEXPRESS: a pilot database from EBI http://www.ebi.ac.uk/arrayexpress/ EXPRESSDB - relational DB of yeast and e. coli expression: http://arep.med.harvard.edu/ExpressDB/ Huge Gene Expression Index (hugeindex.org): from Harvard Institute of Medicine http://www.hugeindex.org/ SMD - Stanford Microarray Database: http://genome-www4.stanford.edu/MicroArray/SMD/ (Univ of) California at San Francisco (DeRisi Lab) http://derisilab.ucsf.edu/publicdata.html Lawrence Berkeley Lab (Eisen Lab) http://rana.lbl.gov/EisenData.htm National Cancer Institute http://discover.nci.nih.gov/nature2000/naturemain.html Princeton Universitycolon cancer http://microarray.princeton.edu/oncology/ Stanford Genome Resource http://genome-www.stanford.edu/cgi-bin/PublicRef Whitehead/MIT http://www.genome.wi.mit.edu/MPR/data_sets.html Genetic Analysis Technology Consortium (GATC):by Molecular Dynamics and Affymetrix http://www.gatconsortium.org/ 四. 分析软件 AMADA (Analyzing Microarray Data): from Univ of Hong Kong http://web.hku.hk/~xxia/software/AMADA.htm ANOVA programs for microarray data: from Churchill's group at Jackson Lab http://www.jax.org/research/churchill/software/anova/index.html CLUSFAVOR (CLUSter and Factor Analysis using Varimax Orthogonal Rotation), from Baylor http://mbcr.bcm.tmc.edu/genepi/ CLUSTER, TREEVIEW: from Eisen's lab at Lawrence Berkeley National Lab http://rana.lbl.gov/EisenSoftware.htm also, http://www.microarrays.org/software.html D-CHIP: specifically for Affymetrix chip data, from Wong's lab at Biostatistic Department,Harvard University http://www.dchip.org GENE-CLUSTER: Whitehead Institute (registration is required). A commercial version of this program is also developed, at Affymetrix http://www.genome.wi.mit.edu/MPR/software.html J-EXPRESS: Univ of Bergen, Norway http://www.ii.uib.no/~bjarted/jexpress/index.html PAGE (PAtterns from Gene Expression): from U Penn. http://www.cbil.upenn.edu/PaGE/ PLAID : from Owen's lab at Stanford Univ. http://www-stat.stanford.edu/~owen/plaid/ SAM (significance analysis of microarrays): from Tibshirani's group at Stanford Univ. http://www-stat.stanford.edu/~tibs/SAM/index.html SAM (significance of array measurement): from Institute for Systems Biology http://www.systemsbiology.org/VERAandSAM/ SMA (Statistic for Microarray Analysis, in R or S-PLUS subroutines): from Speed's lab at Statistics Department of UC Berkeley http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html SVDMAN: from Los Alamos National Laboratory http://public.lanl.gov/mewall/svdman/ TREE-ARRANGE and TREEPS : from Univ Waterloo http://monod.uwaterloo.ca/downloads/treearrange/ VERA (variability and error assessment): from Institute for Systems Biology http://www.systemsbiology.org/VERAandSAM/ XCLUSTER: from Sherlock's lab of Genetics Department of Stanford Univ http://genome-www.stanford.edu/~sherlock/cluster.html public domain programs
- data management
GENEX : from National Center for Genome Resources http://www.ncgr.org/genex/index.html MAPS (MicroArray Project System): from National Institute of Environmental Health Sciences (NIH) http://dir.niehs.nih.gov/microarray/software/maps/ http://www.biostat.harvard.edu/complab/dchip 图象处理：Microarray image processing software sources BioDiscovery Imaging Research National Human Genome Research Institute Stanford University 五.数据分析研究组 Russ Altman , Medicine/Medical Informatics, Stanford Univ Pierre Baldi , Dept Information /Computer Science, Univ California at Irvine Benedikt Brors , Theoretical Bioinformatics, DKFZ, Heidelberg Gary Churchill , The Jackson Lab Jean-Michel Claverie/Stephane Audic , CNRS' Institut de Biologie Structurale et Microbiologie Marseilles, France. Sorin Draghici , Computer Science, Wayne State Univ Michael Eisen , Lawrence Berkeley National Lab Nir Friedman , Computer Science and Engineering, Hebrew Univ David Haussler , Computer Science, Univ California at Santa Cruz Eric Lander/Pablo Tamayo , Whitehead Institute/MIT Michael Newton , Dept Statistics/Biostatistics/Medical Informatics, Univ Wisconsin Walter Ruzzo , Computer Science and Engineering, Univ Washington Mark Segal , Dept Epidemiology and Biostatistics, Univ California at San Francisco. Gavin Sherlock, Dept Genetics, Stanford Univ Richard Simon , Biometric Research Branch, National Cancer Institute, NIH Steve Skiena , Computer Science, SUNY Stony Brook (gene networks) Terry Speed, Dept Statistics, Univ California at Berkeley Roland Somogyi, Molecular Mining Co. (gene networks) Rob Tibshirani/Trevor Hastie/Art Owen , Dept Statistics, Stanford Univ John Weinstein , Genomics and Bioinformatics Group, National Cancer Institute, NIH WingHung Wong , Biostatistics/Statistics, Harvard Univ Zohar Yakhini , Technion - Israel Institute of Technology Richard Young , Whitehead Institute (transcriptional regulatory circuitry) Michael Zhang , Cold Spring Harbor Lab 六.其 他 基因芯片分析方案Protocols for microarray analysis National Human Genome Research Institute Stanford University Telechem University of Pennsylvania 点样机器人Manufacturers of microarray spotting robots Beecher Instruments BioRobotics Genetic Microsystems Gene Machines Genomic Solutions Intelligent Automation Systems Packard 玻片Aminosilane coated slide suppliers Amersham Pharmacia Biotech Corning Costar Telechem 扫描Manufacturers of microarray scanners Axon Beecher Instruments GSI Lumonics Genetic Microsystems Genomic Solutions Molecular Dynamics Virtek |
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