Copyright OpenHelix. No use or reproduction without express written consent1
GAD The Genetic Association Database Materials prepared by: Mary Mangan, Ph.D. Version 2
Copyright OpenHelix. No use or reproduction without express written consent3 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD:
Copyright OpenHelix. No use or reproduction without express written consent4 Introduction GAD Genetic Association Database Associates human genes with diseases See the big picture first, via tables See the specifics next, via detailed records Extensive links to other databases Integrated with UCSC Genome Browser Help curate & add new records Developed by Kevin Becker & team at NIH
Copyright OpenHelix. No use or reproduction without express written consent5 What is Genetic Association? Healthy PopulationDiseased Population Genetic Association: between allele G and the disease. A A A A A G G G G
Copyright OpenHelix. No use or reproduction without express written consent6 Complex Diseases have Complex Associations Healthy PopulationDiseased Population Genetic Association: [ allele G + allele T + smoking ] and the disease G T ++ G T ++ G T ++ G T + G C ++ A T ++
Copyright OpenHelix. No use or reproduction without express written consent7 What about OMIM? Wealth of information Text-based narrative Just hard to visualize alleles and polymorphisms environmental factors genes
Copyright OpenHelix. No use or reproduction without express written consent8 GAD Data 1. Incorporates OMIM - reformats text tables 3. Curates additional data - from less common journals - genetic associations of lower significance - negative data - user-submitted reports 2. Multiple phenotype levels Disease Class Broad Phenotype MeSH Term Narrow Disease Molecular Phenotype 4. Standardizes molecular nomenclature - official gene symbols - official polymorphisms
Copyright OpenHelix. No use or reproduction without express written consent9 GAD Preview Tables Preview the big picture first then select an individual record for details Record
Copyright OpenHelix. No use or reproduction without express written consent10 GAD Homepage PMID: Feedback PMC:
Copyright OpenHelix. No use or reproduction without express written consent11 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD:
Copyright OpenHelix. No use or reproduction without express written consent12 GAD Views click
Copyright OpenHelix. No use or reproduction without express written consent13 Gene View, part 1 Data Column official gene symbol Data Columns icon links unique genetic association
Copyright OpenHelix. No use or reproduction without express written consent14 Links and Field Descriptions Field Descriptions Explains each data field
Copyright OpenHelix. No use or reproduction without express written consent15 Gene View, part 2 SCROLL to see more... Genetic Association? Disease Class
Copyright OpenHelix. No use or reproduction without express written consent16 A2M Detailed Record More links
Copyright OpenHelix. No use or reproduction without express written consent17 Disease View Disease data highlighted click to open Disease View for CAD
Copyright OpenHelix. No use or reproduction without express written consent18 Coronary Artery Disease View SCROLL to see more...
Copyright OpenHelix. No use or reproduction without express written consent19 Chromosome View
Copyright OpenHelix. No use or reproduction without express written consent20 Environmental Factor and Gene Interaction View environmental factors
Copyright OpenHelix. No use or reproduction without express written consent21 Simple Search click HMOX1 TIP: always use official gene nomenclature!
Copyright OpenHelix. No use or reproduction without express written consent22 HMOX1 Gene View Total records
Copyright OpenHelix. No use or reproduction without express written consent23 HMOX1 Positive Data Only from “total” to just “positive” all Y TIP: just be sure to Reset for next query
Copyright OpenHelix. No use or reproduction without express written consent24 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD:
Copyright OpenHelix. No use or reproduction without express written consent25 Advanced Search SCROLL for over 60 field options IMPORTANT: GAD remembers the last query you did. If last query was Disease-related, then you get a Disease-restricted query page click “Reset”
Copyright OpenHelix. No use or reproduction without express written consent26 Advanced Query Example prostate cancer Japanese smoking click scroll
Copyright OpenHelix. No use or reproduction without express written consent27 Batch Search pick-list paste in gene list
Copyright OpenHelix. No use or reproduction without express written consent28 Batch Search Results Disease Classes (see “Links” for abbreviations) TotalIMM NEURPSY
Copyright OpenHelix. No use or reproduction without express written consent29 Analyzing Large Gene Sets Disease Classes Immune Inflammation Neurological
Copyright OpenHelix. No use or reproduction without express written consent30 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD:
Copyright OpenHelix. No use or reproduction without express written consent31 Add a Record
Copyright OpenHelix. No use or reproduction without express written consent32 Become an Expert
Copyright OpenHelix. No use or reproduction without express written consent33 Download GAD
Copyright OpenHelix. No use or reproduction without express written consent34 GAD Track on UCSC Browser turn GAD track on to see data integrated with browser
Copyright OpenHelix. No use or reproduction without express written consent35 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD:
Copyright OpenHelix. No use or reproduction without express written consent36 GAD Summary Tables Record
Copyright OpenHelix. No use or reproduction without express written consent37 GAD: View from Different Perspectives DiseaseGene Polymorphism Reference Environmental Factor ALL Scroll...
Copyright OpenHelix. No use or reproduction without express written consent38 GAD: Searches Basic keyword reference gene disease Multiple Options input gene list Batch Query
Copyright OpenHelix. No use or reproduction without express written consent39 GAD: Other Features Add recordsBecome an Expert GAD on UCSC Browser Download GAD
Copyright OpenHelix. No use or reproduction without express written consent40 GAD Agenda Introduction and Credits Basic Search Advanced Search Other Features Summary Exercises GAD:
Copyright OpenHelix. No use or reproduction without express written consent41