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Example of a Functional Genomics Study
Molecular Ecology 2006 15, 4635-4643
Drosophila
• Most species are very poor ecological
model organisms.
• D. mojavensis is cactophilic: it uses 4
different kinds of cactus host in the
Sonoran Desert.
• Oviposits in necrotic tissues, exposing
larvae to varied toxic chemicals.
Objective
Identify gene expression differences of 3rd instar
larvae reared between two chemically distinct
cactus hosts:
•Agria (Stenocereus gummosus), native host
•Organpipe (Stenocereus thurberi), alternative host
Used a custom microarray (6520 anonymous
cDNA fragments that were pinned robotically
to glass slides)
Organpipe vs
Agria Cacti
• Differ in lipids, triterpenes, and glycosides.
•Differ in alcohol content.
•Adh is duplicated in D. mojavensis and
The paralogs are known to play different
roles in host adaptation.
Mixed Model Anova Approach
1)
Relative
hybridization
Intensity
= Random Technical and Residual
Variation
Yij = µ + ARRAYi + DYEj + ARRAY × DYEij + Residualij
2)
Residual
Variation
Per Gene
= Random Technical and Fixed
Technical and Biological Variation
Residualijkl = µ + ARRAYi + DYEj + CACTUS + ARRAY x
Spotil + Errorijkl
Correcting for Multiple Tests
Bonferroni correction: More conservative test where
the significance threshold is divided by the total
number of tests.
False Discovery Rate (FDR): Less conservative test
that calculates the number of false positives within
a set of significant values (P<0.05) and then
calculates a new significance threshold , q.
Identifying Differentially Expressed Genes
Greater Expression Organpipe
Greater Expression Agria
P value for
Each Gene
Specific Anova
-log(P)
Bonferroni (173)
False Discovery
Rate (1034)
Fold Difference Log2
Representation of Up-regulated
Genes Among Gene Ontology
Categories.
Conclusions
(i) Cactus host usage affects patterns of gene
transcription.
(ii) Loci whose function involve detoxification
were differentially regulated in response to a
cactus host shift.
(iii) A subset of the differentially expressed
loci may have arisen de novo in the D.
mojavensis lineage.