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Web-Link Name Reference DRSC Flockhart I, Booker M, Kiger A, Et Al.: Flyrnai: the Drosophila Rnai Screening Center Database

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web-link Name Reference http://flyrnai.org/cgi-bin/RNAi_screens.pl DRSC Flockhart I, Booker M, Kiger A, et al.: FlyRNAi: the Drosophila RNAi screening center database. Nucleic Acids Res. 34(Database issue):D489-94 (2006) http://flybase.bio.indiana.edu/ FlyBase Grumbling G, Strelets V.: FlyBase: anatomical data, images and queries. Nucleic Acids Res. 34(Database issue):D484-8 (2006) http://rnai.org/ RNAiDB Gunsalus KC, Yueh WC, MacMenamin P, et al.: RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res. 32(Database issue):D406-10 (2004) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIMOMIM Hamosh A, Scott AF, Amberger JS, et al.: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33(Database issue):D514-7 (2005) http://www.phenomicdb.de/ PhenomicDB Kahraman A, Avramov A, Nashev LG, et al.: PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics. 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Nucleic Acids Res. 32(Database issue):D311-4 (2004) http://www.pharmgkb.org/ PharmGkb Thorn CF, Klein TE, Altman RB.: PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods Mol Biol. 311:179-91 (2005) http://www-deletion.stanford.edu/YDPM/YDPM_index.htmlYDPM Prokisch H, Scharfe C, Camp DG 2nd, et al.: Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol. 2(6):e160 (2004) http://www.ebi.ac.uk/arrayexpress/ ArrayExpress Brazma A, Parkinson H, Sarkans U, et al.: ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31(1):68-71 (2003) http://staffa.wi.mit.edu/chipdb/public/ ChipDB http://twod.med.harvard.edu/ExpressDB/ ExpressDB Aach J, Rindone W, Church GM.: Systematic management and analysis of yeast gene expression data. Genome Res. 10(4):431-45 (2000) http://symatlas.gnf.org/SymAtlas/ Gene Expression Atlas Su AI, Wiltshire T, Batalov S, et al.: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 101(16):6062-7 (2004) http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus Barrett T, Suzek TO, Troup DB, et al.: NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 33(Database issue):D562-6 (2005) http://www.germonline.org/ GermOnline Primig M, Wiederkehr C, Basavaraj R, et al.: GermOnline, a new cross-species community annotation database on germ-line development and gametogenesis. Nat Genet. 35(4):291-2 (2003) http://www.biotechnologycenter.org/hio/ Human Gene Expression Index Haverty PM, Weng Z, Best NL, et al.: HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Res. 30(1):214-7 (2002) http://www.dkfz-heidelberg.de/mchips/ M-CHiPS Fellenberg K, Hauser NC, Brors B, et al.: Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis. Bioinformatics 18(3):423-33 (2002) http://affymetrix.arabidopsis.info/narrays/experimentbrowse.plNASCArrays Craigon DJ, James N, Okyere J, et al.: NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 32(Database issue):D575-7 (2004) http://www.oncomine.org/main/index.jsp Oncomine Rhodes DR, Yu J, Shanker K, et al.: ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 6(1):1-6 (2004) http://read.gsc.riken.go.jp/ Riken Expression Array Database Bono H, Kasukawa T, Hayashizaki Y, et al.: READ: RIKEN Expression Array Database. Nucleic Acids Res. 30(1):211-3 (2002) http://red.dna.affrc.go.jp/RED/ Rice Expression Database Yazaki J, Kishimoto N, Ishikawa M, et al.: Rice Expression Database: the gateway to rice functional genomics. Trends in Plant Science 7 (12):563-564 (2002) http://psi081.ba.ars.usda.gov/SGMD/default.htmSoybean Genomics and Microarray DatabaseAlkharouf NW, Matthews BF.: SGMD: the Soybean Genomics and Microarray Database. Nucleic Acids Res. 32(Database issue):D398-400 (2004) http://genome-www5.stanford.edu/ Stanford Microarray Database Sherlock G, Hernandez-Boussard T, Kasarskis A, et al.: The Stanford Microarray Database. Nucleic Acids Res. 29(1):152-5 (2001) http://info.med.yale.edu/microarray/ Yale Microarray Database Cheung KH, White K, Hager J, et al.: YMD: a microarray database for large-scale gene expression analysis. 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  • Mappfinder: Using Gene Ontology and Genmapp to Create a Global

    Mappfinder: Using Gene Ontology and Genmapp to Create a Global

    Method Open Access MAPPFinder: using Gene Ontology and GenMAPP to create a comment global gene-expression profile from microarray data Scott W Doniger*, Nathan Salomonis*, Kam D Dahlquist*†, Karen Vranizan*‡, Steven C Lawlor* and Bruce R Conklin*†§ Addresses: *Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94141-9100, USA. †Cardiovascular Research Institute, and §Departments of Medicine and Cellular and Molecular Pharmacology, University of California, San Francisco, ‡ CA 94143, USA. Functional Genomics Lab, University of California, Berkeley, CA 94720, USA. reviews Correspondence: Bruce R Conklin. E-mail: [email protected] Published: 6 January 2003 Received: 11 September 2002 Revised: 8 October 2002 Genome Biology 2003, 4:R7 Accepted: 8 November 2002 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2003/4/1/R7 reports © 2003 Doniger et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. Abstract deposited research MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP (http://www.GenMAPP.org). The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene- expression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged.