Copyright OpenHelix. No use or reproduction without express written consent1
DAVID Database for Annotation, Visualization and Integrated Discovery Materials prepared by: Cynthia Perreault-Micale, Ph.D. Updated: Q Version 2.0
Copyright OpenHelix. No use or reproduction without express written consent3 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID:
Homepage access: Copyright OpenHelix. No use or reproduction without express written consent4 Introduction DAVID Database of Annotation, Visualization, and Integrated Discovery free, web-based bioinformatics tool extracts biological meaning from genes covers all species developed by Lempicki & colleagues (NIAID)
Copyright OpenHelix. No use or reproduction without express written consent5 Making Sense of Large Gene Lists 1456 genes upregulated 2846 genes downregulated microarray but what does it all mean? secreted proteins defensive response involved in
Copyright OpenHelix. No use or reproduction without express written consent6 DAVID Gene Concept UniProt: P84215 UniProt: Q73415 SwissProt: ABC UniProt PIR RefSeq: NM_2355 UniProt: N66532 GenPep: AA63554 Entrez-Gene Gene: ABC1 SwissProt: ABC GO: cytoplasm GO: limb development GO: kinase UniProt: RefSeq: NM_ RefSeq: NM_2355 DAVID gene UniProt: P84215 UniProt: Q73415 Gene: ABC1 SwissProt: ABC GO: cytoplasm GO: limb development GO: kinase UniProt: RefSeq: NM_ RefSeq: NM_2355 UniProt: N66532 GenPep: AA63554 Most complete set of annotations
Copyright OpenHelix. No use or reproduction without express written consent7 90 Million Annotations! Taken from: Sherman et al., BMC Bioinformatics (2007) 8: million from Ontologies, such as GO
Copyright OpenHelix. No use or reproduction without express written consent8 DAVID Homepage
Copyright OpenHelix. No use or reproduction without express written consent9 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID:
Copyright OpenHelix. No use or reproduction without express written consent10 Starting DAVID
Copyright OpenHelix. No use or reproduction without express written consent11 Upload a Gene List Tab delimited text file how to make a file “Save As...”
Copyright OpenHelix. No use or reproduction without express written consent12 Upload a Gene List, continued numerous gene ID options or “Not Sure” or official gene symbols
Copyright OpenHelix. No use or reproduction without express written consent13 Pre-Loaded Affymetrix Background Lists Background Chip Options Scroll to:
Copyright OpenHelix. No use or reproduction without express written consent14 Resveratrol Example >300 genes tab-delimited text file (.txt)
Copyright OpenHelix. No use or reproduction without express written consent15 Selecting Species and Renaming the File
Copyright OpenHelix. No use or reproduction without express written consent16 Show Gene List detailed gene report functionally related genes
Copyright OpenHelix. No use or reproduction without express written consent17 Which Tool?
Copyright OpenHelix. No use or reproduction without express written consent18 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID:
Copyright OpenHelix. No use or reproduction without express written consent19 click Annotation Categories Disease General Literature Pathways Protein Domains Protein Interactions
Copyright OpenHelix. No use or reproduction without express written consent20 Functional Annotation Tool default Click here
Copyright OpenHelix. No use or reproduction without express written consent21 GO Category Details = 96.6% OPTION : select different levels of GO BP_4 BP_3 BP_2 BP_1 GO-BP Levels
Copyright OpenHelix. No use or reproduction without express written consent22 GO Category Details, part 2 list of all 314 genes
Copyright OpenHelix. No use or reproduction without express written consent23 Functional Annotation Chart (for a Category) Related Terms Genes that have this GO-BP annotation
Copyright OpenHelix. No use or reproduction without express written consent24 Functional Annotation Options at least 2 genes must be annotated to the term range = (lower = more enriched) additional statistical display options
Copyright OpenHelix. No use or reproduction without express written consent25 Show Me All the Annotations! lists all annotations from every selected category
Copyright OpenHelix. No use or reproduction without express written consent26 Functional Annotation Chart (Total) Page Page 2 > 1,600 annotations
Copyright OpenHelix. No use or reproduction without express written consent27 Functional Annotation Clustering
Copyright OpenHelix. No use or reproduction without express written consent28 Functional Annotation Clustering Results Enrichment Scores “apoptosis” annotations clustered into functional groups
Copyright OpenHelix. No use or reproduction without express written consent29 Functional Annotation Clustering Details Genes associated with term Genes associated with Cluster 1
Copyright OpenHelix. No use or reproduction without express written consent30 Functional Annotation Clustering Options edit threshold levels to change stringency and clustering parameters
Copyright OpenHelix. No use or reproduction without express written consent31 Heat Maps 6 annotations15 genes click
Copyright OpenHelix. No use or reproduction without express written consent32 Heat Map Display 15 genes 6 annotations
Copyright OpenHelix. No use or reproduction without express written consent33 Making Biological Sense resveratrol >300 genes DAVID
Copyright OpenHelix. No use or reproduction without express written consent34 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID:
Copyright OpenHelix. No use or reproduction without express written consent35 Gene Functional Classification Tool click
Copyright OpenHelix. No use or reproduction without express written consent36 Gene Functional Classification Results clusters genes into functional groups edit threshold levels to change stringency and clustering parameters
Copyright OpenHelix. No use or reproduction without express written consent37 Gene Functional Classification Icons Gene Report heat map Related Genes Term Report
Copyright OpenHelix. No use or reproduction without express written consent38 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID:
Copyright OpenHelix. No use or reproduction without express written consent 39 Create a Sublist new sublist
Copyright OpenHelix. No use or reproduction without express written consent40 Gene ID Conversion Tool click
Copyright OpenHelix. No use or reproduction without express written consent41 Gene ID Conversion Results inputoutput
Copyright OpenHelix. No use or reproduction without express written consent42 Gene Name Batch Viewer
Copyright OpenHelix. No use or reproduction without express written consent43 Gene Name Batch Viewer Gene List upload list
Copyright OpenHelix. No use or reproduction without express written consent44 Gene Name Batch Viewer Results
Copyright OpenHelix. No use or reproduction without express written consent45 Pathway Viewer = genes in your list
Copyright OpenHelix. No use or reproduction without express written consent46 Disease Analysis GAD OMIM GAD_CLASS
Copyright OpenHelix. No use or reproduction without express written consent47 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID:
Copyright OpenHelix. No use or reproduction without express written consent48 DAVID: Gene Lists --> Annotations Extracts Annotations Annotations
Copyright OpenHelix. No use or reproduction without express written consent49 DAVID: Discover the Biology > 1600 Annotations > 100 Functional Clusters Group Annotations into Functional Clusters apoptosis cell cycle development
Copyright OpenHelix. No use or reproduction without express written consent50 DAVID: Convert IDs --> Symbols --> Clusters 120 Gene Symbols Convert IDs into Symbols 3 Gene Clusters Gene Lists into Gene Clusters
Genes Copyright OpenHelix. No use or reproduction without express written consent51 DAVID: Integrated Data, Seamless Navigation
Copyright OpenHelix. No use or reproduction without express written consent52 DAVID: Visualize Data in a New Way Heat Maps Pathway Maps
Copyright OpenHelix. No use or reproduction without express written consent53 DAVID Agenda Introduction and Credits Upload a Gene List Functional Annotation Tool Gene Functional Classification Tool Other Features Summary Exercises DAVID:
Copyright OpenHelix. No use or reproduction without express written consent54