Introduction to DNA Microarrays: Functional Mining

of Array Patterns

Michael F. Miles, M.D., Ph.D.

Depts. of Pharmacology/Toxicology and Neurology and the Center for Study of Biological Complexity

mfmiles@vcu.edu

225-4054

Tertiary Analysis: Connecting Function with Expression Patterns

• Annotation– UniGene/Swiss-Prot, SOURCE, CARS

• Biased functional assessment– Functional group interrogation

Manual, GenMAPP, GeneSpring

• Non-biased functional queries– PubGen– MAPPFinder, DAVID/Ease, GEPAS, others– Cytoscape

• Overlaying genomics and genetics– WebQTL

CARS: A Curated Annotation Database Tool

Tertiary Analysis: Connecting Function with Expression Patterns

• Annotation– UniGene/Swiss-Prot, SOURCE, CARS

• Biased functional assessment– Functional group interrogation

• Manual, GenMAPP, GeneSpring

• Non-biased functional queries– PubGen– MAPPFinder, DAVID/Ease, GEPAS, others– Cytoscape

• Overlaying genomics and genetics– WebQTL

Mirnics et al., Neuron 28:53, 2000

Microarray Analysis of Gene Expression in Prefrontal Cortex of Schizophrenics

0

2

4

6

8

10

12

S-Score

Ribosomal

Total

p< 10-33 (Chi-Square)

Distribution of Expressed Genes across Seven Frontal Cortex Comparisons

Percent of Change ALL Frontal MYEL GLU PSYN APOP Cell cycleAlcRes

(44029) (120) (50) (511) (618) (752) (733)

<=-1.9 0.7 4.2 2.0 1.2 0.3 1.1 1.4-1.6 to -1.89 1.9 8.3 6.0 2.0 1.5 2.7 3.3-1.59 to 1.59 94.9 75.8 86.0 93.9 96.0 94.7 92.0

1.6 to 1.89 1.8 4.2 6.0 2.5 2.1 1.2 2.3>=1.9 0.7 7.5 0.0 0.4 0.2 0.4 1.1

Chi-square, p< NA <<0.0001 0.0002 0.95 0.94 0.93 0.72

Functional Hierarchy Statistics in Alcoholic Brain Tissue(Frontal Cortex)

Courtesy of Dr. Adron Harris, UT at Austin

Non-biased (semi) Functional Group Analysis: GenMAPP

Tertiary Analysis: Connecting Function with Expression Patterns

• Annotation– UniGene/Swiss-Prot, SOURCE, CARS

• Biased functional assessment– Functional group interrogation

• Manual, GenMAPP, GeneSpring

• Non-biased functional queries– PubGen– MAPPFinder, DAVID/Ease, GEPAS, others– Cytoscape

• Overlaying genomics and genetics– WebQTL

Efforts to Integrate Diverse Biological Databases

with Expression Information: PubGen

www.PubGen.org

Tertiary Analysis: Connecting Function with Expression Patterns

• Annotation– UniGene/Swiss-Prot, SOURCE, CARS

• Biased functional assessment– Functional group interrogation

• Manual, GenMAPP, GeneSpring

• Non-biased functional queries– PubGen– MAPPFinder, DAVID/Ease, GEPAS, others– Cytoscape

• Overlaying genomics and genetics– WebQTL

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QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.

Expression of Aldh9a1 Across BxD RI Lines

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WebQTL Allows Definition of Genetic “Linkage” for Expression Patterns

Expression Profiling:

“It is possible that the expression profile could serve as a universal phenotype … Using a comprehensive database of reference profiles, the pathway(s) perturbed by an uncharacterized mutation would be ascertained by simply asking which expression patterns in the database its profile most strongly resembles … it should be equally effective at determining consequences of pharmaceutical treatments and disease states”

Hughes et al. Cell 102:109-126 (2000)

Use of Expression Profile “Compendium” to Characterize Gene or Drug Function

Hughes et al. Cell 102:109-126 (2000)

established error modelprofiled large number of mutants/drugs under highly controlled conditionsstatistical treatment of expression patternsverified array results with biochemical/phenotypic assays

Key features:

Correlation in Expression Profiles of Drugs/Genes Affecting Same

Pathways

cup5 and vma8, components of

H+/ATPase complex

Unrelated gene

mutants HMG CoA-

reductase mutant vs. lovastatin, an

inhibitor of HMG2

Red symbols = significant change (p<0.05) in both treatmentsHughes et al. Cell 102:109-126 (2000)

Assigning Function to Uncharacterized Genes by Expression Profiles

Hughes et al. Cell 102:109-126 (2000)

Expression Networks

Expression Profiling

Pharmacology Genetics

Behavior

Prot-Prot

Interactions

OntologyHomoloGene

BioMed Lit

Relations