A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Reverter et al Bioinformatics 21:1112 Validation of alternative methods of data normalization in gene co-expression studies

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Motivation Statistics are like a bikini, what they reveal is suggestive, but what they conceal is vital. Aaron Levenstein

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Motivation Correlations Are Dangerous! # # # # ## # # # # # # # # # # # # # # ## # # # # # # # # # Exp 1 Exp 2 Gene 1 Gene 2 Gene 1 Gene 2 # # # # # # # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Introduction Validation of alternative methods of data normalization in gene co-expression studies. Bioinformatics 2005, 21:1112 A. Reverter, W. Barris, S.M. McWilliam, K.A. Byrne, Y.H. Wang, S.H. Tan, N. Hudson, and B.P. Dalrymple Experiment a Hybs.Cond.Signals b NMeanSTD 1. Two breeds by two diets74193, Three diets143361, Two diets at three ages246801, Two breeds at three ages186459, Two fat treatments at two ages154418, Expression of each clone (gene) across 23 conditions

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Introduction Armidale Animal Breeding Summer Course, UNE, Feb

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization ############################################ Clone i Experiment 1 (  E1,  E1 ) Experiment 2 (  E2,  E2 ) Cond (  Ci,  Ci ) 1. RMNA 2. RMCE3. RMEC Expression of each clone (gene) across 23 conditions

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization Expression of each clone (gene) across 23 conditions

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization Expression of each clone (gene) across 23 conditions

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization Expression of each clone (gene) across 23 conditions

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization Expression of each clone (gene) across 23 conditions

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization Expression of each clone (gene) across 23 conditions Expected to be the equal!

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization Log2 Intensities Comparison Group Array|Block|Dye (FIXED) Main Gene Effect (RANDOM) Gene x Variety (RANDOM) Residual (RANDOM) DE Genes Gene x Array|Block (RANDOM) Gene x Dye (RANDOM) Mixed-Model Equations

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization 4. MM1NA 5. MM1CE6. MM1EC 7. MM5NA 8. MM5CE9. MM5EC

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Methods Nine Methods of Data Normalization 4. MM1NA 5. MM1CE6. MM1EC 7. MM5NA 8. MM5CE9. MM5EC Vector of BLUP Clone x Condition Interaction

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Observed (RED) vs Expected (BLUE) Results

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Results Average across all pair-wise gene correlations (bold, italics and on the diagonal); Correlation of correlations (above diagonal); and maximum absolute discrepancy between methods (below diagonal) RMNA RMCE RMEC MM1NA MM1CE MM1EC MM5NA MM5CE MM5EC

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Results Redundant genes (ie. those with many probes on the array) allow for Validation

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Results Redundant genes allow for Validation

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Results 624 Gene Co-Expression (Alphabetical order) Robisomal Proteins

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Brian Sigrid Siok Kwee Keren Applications

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Applications False Discovery Rate as a Function of Correlation

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Applications DLK1 COL3A1 LUM GNAI2 DCAL1 CIDEC KARS UBA52 TNFRSF Callipyge Mutation

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Applications DLK1 COL3A1 LUM GNAI2 DCAL1 CIDEC KARS UBA52 TNFRSF21 DES FN1 CTSF SPARC CAV1 ACTA1 TM4SF Callipyge Mutation

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Applications DLK1 COL3A1 LUM GNAI2 DCAL1 CIDEC KARS UBA52 TNFRSF21 DES FN1 CTSF SPARC CAV1 ACTA1 TM4SF2 MYBPC2 MYL1 LDHA PGK1 CASQ Callipyge Mutation

A Quantitative Overview to Gene Expression Profiling in Animal Genetics Armidale Animal Breeding Summer Course, UNE, Feb Co-Expression Applications DLK1 COL3A1 LUM GNAI2 DCAL1 CIDEC KARS UBA52 TNFRSF21 DES FN1 CTSF SPARC CAV1 ACTA1 TM4SF2 MYBPC2 MYL1 LDHA PGK1 CASQ ITM2B ENO3 PYGM GPI CKM Callipyge Mutation