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Example of a Functional Genomics Study

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

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Example of a Functional Genomics Study

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  1. Example of a Functional Genomics Study Molecular Ecology 2006 15, 4635-4643

  2. 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.

  3. 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)

  4. 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.

  5. Mixed Model Anova Approach Relative hybridization Intensity 1) = Random Technical and Residual Variation Yij = µ + ARRAYi + DYEj + ARRAY × DYEij + Residualij Residual Variation Per Gene 2) = Random Technical and Fixed Technical and Biological Variation Residualijkl = µ + ARRAYi + DYEj + CACTUS + ARRAY x Spotil + Errorijkl

  6. 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.

  7. 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

  8. Representation of Up-regulated Genes Among Gene Ontology Categories.

  9. 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.

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