DAVID

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DAVID

• The Database for Annotation, Visualization and
  Integrated Discovery

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Microarray analysis output List of
differentially expressed genes upregulated down
regulated List of genes from an interesting
cluster
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http//obo.sourceforge.net/
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http//www.geneontology.org
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GO Evidence Codes
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Gene Ontology
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Ashburner et al. Nature Genetics 25, 25 (2000)
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Pathway Databases

• KEGG - http//www.genome.jp/kegg/kegg2.html
• BioCarta - http//www.biocarta.com/index.asp

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KEGG

• KEGG Home Page
• Go to Metabolism of Complex Lipids ?
  Phospholipid Degradation.
• Press on the gene 3.1.4.4 (Phospholipase D).
• Press on phosphatidylcholine and phosphatidic
  acid (PA).
• From PA, go to the PI signaling system.

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Nature Immunology 5, 1181 - 1189 (2004)
GEO GDS776 Data Set
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Experimental Design Gene Expression in human
macrophages
Priming
Stimulation
P lt 0.05
48 genes
Up X2
Up X2
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DAVID

• http//david.niaid.nih.gov/david/version2/index.ht
  m

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http//david.niaid.nih.gov/david/version2/index.ht
m
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35061_at 37219_at 33304_at 36804_at 32056_at 31343
_at 1761_at 35648_at 36776_at 1737_s_at 425_at 397
81_at 32249_at 31355_at 717_at 41027_at 34214_at 3
5947_at 37168_at 40323_at 39660_at 34594_at 36886_
f_at 1852_at
48 probe sets
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Make sure you have

• Go terms (BP, MF, CC), level 4
• InterPro Name
• KEGG Pathway
• BioCarta

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USER_AFFY_ID  245_at SPECIES  Homo sapiens Temp
DAVID ID  481389 
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Functional classification of the genes in the list

• Statistical test for over-representation of
  functional categories in the list

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KEGG - CYTOKINE-CYTOKINE RECEPTOR
INTERACTION(Homo sapiens)
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BioCarta - Adhesion and Diapedesis of
Granulocytes(Homo sapiens)
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http//www.pdg.cnb.uam.es/UniPub/iHOP/
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Thank you!
Vered Caspi
http//bioinfo.bgu.ac.il
veredcc_at_bgumail.bgu.ac.il