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Saccharomyces Genome Database (SGD) The Yeast Model Organism Database for Saccharomyces cerevisiae Materials prepared by: Dorothy S. Reilly, Ph.D. Jennifer M. Williams, Ph.D. Updated: Q Version 3
Copyright OpenHelix. No use or reproduction without express written consent3 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent4 Introduction to SGD Saccharomyces Genome Database: “SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.” Vast collection of well-organized yeast information! Official nomenclature arbiter
Copyright OpenHelix. No use or reproduction without express written consent5 History of SGD History & Growth Newsletter Archive
Homepage “Publications” link Copyright OpenHelix. No use or reproduction without express written consent6 SGD Publications Citing SGD:
Copyright OpenHelix. No use or reproduction without express written consent7 SGD Acknowledgements & Funding SGD Suggestions and Questions On most pages
Copyright OpenHelix. No use or reproduction without express written consent8 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent9 SGD Organization & Navigation Click Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent10 SGD Help Resources SGD web form or Click
Copyright OpenHelix. No use or reproduction without express written consent11 SGD Site Map
Copyright OpenHelix. No use or reproduction without express written consent12 Site Map Help
SGD Site Navigation Saccharomyces Genome Database: Contact SGD SGD web form or search help
Copyright OpenHelix. No use or reproduction without express written consent14 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent15 drug Basic Search & Display Gene & Protein Information Functional Information Colleagues & Authors IDs at External Resources
Copyright OpenHelix. No use or reproduction without express written consent16 SGD Locus Summary ERG5 Locus Summary Page Basic information ERG5 resources Pulldown menus References for this page Gene summary paragraph Subject tabs Subject tabs, pulldown menus, and links to additional information Additional information
Copyright OpenHelix. No use or reproduction without express written consent17 ERG5 Basic Info, Top Names, Aliases & Feature Type Yeast Systematic Names: YMR015C Y = “Yeast” M = letter representing chromosome number (1=A) R = Right or Left arm of chromosome 015 = relative position of ORF from centromere C = Watson or Crick strand Gene Ontology & Pathway Annotations
Phenotypes ERG5 Basic Info, Middle Interactions Copyright OpenHelix. No use or reproduction without express written consent18
Copyright OpenHelix. No use or reproduction without express written consent19 ERG5 Basic Info, Bottom Sequences
Copyright OpenHelix. No use or reproduction without express written consent20 ERG5 Locus Summary, Lower References Cited
Copyright OpenHelix. No use or reproduction without express written consent21 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent22 ERG5 Locus Summary, Right Panel SGD ORF map & GBrowse access to many resources from pulldown menus Expression Summary histogram
Copyright OpenHelix. No use or reproduction without express written consent23 Locus Page Pull-Down Menus
Copyright OpenHelix. No use or reproduction without express written consent24 SGD Locus Page Tabs Summary Locus History Literature Gene Ontology Phenotype Interactions Expression Protein Wiki
25 Locus Tabs: Locus History, Literature, GO Curation Types: Manual High-throughput Computational Molecular Function Biological Process Cellular Component Copyright OpenHelix. No use or reproduction without express written consent
26 Locus Tabs: Mutant Phenotypes, Interactions Add data filter Scroll to:
Copyright OpenHelix. No use or reproduction without express written consent Locus Tabs: Expression, Protein, Wiki 27 Log in or create an account
Copyright OpenHelix. No use or reproduction without express written consent28 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent29 SGD Search Options Every search option is different If you want it, it’s probably there! Advanced & SGD web page searches Search Yeast Literature Search Gene Function Info Search Protein Info Search Colleague Info Basic Search Gene & Sequence Searches
Copyright OpenHelix. No use or reproduction without express written consent30 Basic Search Advanced Search Link Google Search Advanced Search 1) Chromosomal Feature 2) Property Filters: Annotation/sequence Protein Phenotype Interaction GO Annotations Large-scale
Copyright OpenHelix. No use or reproduction without express written consent31 YeastMine A project with InterMine, RGD, & ZFIN Allows interoperability between MODs Powerful & flexible search interface Quick Search, Templates, QueryBuilder Homepage left menu FAQs Help Quick Search
Copyright OpenHelix. No use or reproduction without express written consent32 YeastMine – Lists Example click rad51; rad52; rad53; ddc1; rad55; rad57; spo11; dmc1; rad17; rad9; rad24; msh1; msh5; mre11; xrs2; ndt80; tid1; ssb1; pre3; acr1; doa3; rad54; ssf1 upload Example list of 23 yeast gene names
Copyright OpenHelix. No use or reproduction without express written consent33 YeastMine – Confirm List add click
Copyright OpenHelix. No use or reproduction without express written consent34 YeastMine –List Analysis List Summary Information Widgets List Template Queries Log in to save Lists, query results, etc.
Biochemical Pathway Search allantoin Copyright OpenHelix. No use or reproduction without express written consent35
Copyright OpenHelix. No use or reproduction without express written consent36 Global Gene Hunter Databases searched: SGD, PubMed, Entrez Nucleotide, PDB, PIR, etc. Gene Name Additional Filters
Copyright OpenHelix. No use or reproduction without express written consent37 Textpresso Literature Search drug resistance Enter term Reference Information Abstract Matching Sentences Supplemental Info
Copyright OpenHelix. No use or reproduction without express written consent38 Advanced Search Summary Many search types, lots of information to find!
Copyright OpenHelix. No use or reproduction without express written consent39 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent40 GO Resources - GO Slim Mapper Homepage left menu
Copyright OpenHelix. No use or reproduction without express written consent41 Submit Data Homepage left menu
Homepage left menu Copyright OpenHelix. No use or reproduction without express written consent42 Download Data
Copyright OpenHelix. No use or reproduction without express written consent43 Yeast Genome Wiki Wiki Background Information includes: General S. cerevisiae information Educational resources S. pombe information Candida albicans information Links to other fungal information Fungal genome sequencing projects Fungal genome database projects
Copyright OpenHelix. No use or reproduction without express written consent44 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent45 Summary Extensive collection of data & tools Model organism specific focus If you want it, it’s probably there! You’ll receive a prompt reply! Contact SGD
SGD - Extensive Data & Tools Available SGD: So Much to Offer! Copyright OpenHelix. No use or reproduction without express written consent46
Copyright OpenHelix. No use or reproduction without express written consent47 SGD Agenda Introduction & Credits Organization & Navigation Basic Search & Display Additional Gene Information Advanced Searches Other Resources Summary Exercises Saccharomyces Genome Database:
Copyright OpenHelix. No use or reproduction without express written consent48