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A Quantitative Overview to Gene Expression Profiling in Animal Genetics

A Quantitative Overview to Gene Expression Profiling in Animal Genetics. Co-Expression. Validation of alternative methods of data normalization in gene co-expression studies. Reverter et al. 2005 Bioinformatics 21:1112. Armidale Animal Breeding Summer Course, UNE, Feb. 2006.

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A Quantitative Overview to Gene Expression Profiling in Animal Genetics

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  1. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Validation of alternative methods of data normalization in gene co-expression studies Reverter et al. 2005 Bioinformatics 21:1112 Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  2. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Motivation Statistics are like a bikini, what they reveal is suggestive, but what they conceal is vital. Aaron Levenstein Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  3. A Quantitative Overview to Gene Expression Profiling in Animal Genetics # # # # # # # # # # # # # # # # # # # # # # Gene 2 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # Gene 1 Exp 2 Exp 1 Co-Expression Motivation Correlations Are Dangerous! # # # # # # # # # Gene 2 # # # # # # # # # # # # # # # # # # # # # # Gene 1 Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  4. A Quantitative Overview to Gene Expression Profiling in Animal Genetics 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 Expression of each clone (gene) across 23 conditions Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  5. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Introduction 1 4 2 5 3 Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  6. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Expression of each clone (gene) across 23 conditions Nine Methods of Data Normalization 1. RMNA 2. RMCE 3. RMEC Clone i Cond # # # # # # ################ 1 Experiment 1 (E1, E1) 2 3 4 Experiment 2 (E2, E2) 5 (Ci, Ci) Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  7. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Expression of each clone (gene) across 23 conditions Nine Methods of Data Normalization Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  8. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Expression of each clone (gene) across 23 conditions Nine Methods of Data Normalization Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  9. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Expression of each clone (gene) across 23 conditions Nine Methods of Data Normalization Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  10. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Expression of each clone (gene) across 23 conditions Nine Methods of Data Normalization Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  11. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Expression of each clone (gene) across 23 conditions Nine Methods of Data Normalization Expected to be the equal! Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  12. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Nine Methods of Data Normalization Log2 Intensities Mixed-Model Equations Residual (RANDOM) Gene x Dye (RANDOM) Gene x Variety (RANDOM) Comparison Group Array|Block|Dye (FIXED) Main Gene Effect (RANDOM) Gene x Array|Block (RANDOM) DE Genes Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  13. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Nine Methods of Data Normalization 4. MM1NA 5. MM1CE 6. MM1EC Based on Uni-variate Mixed-Models 7. MM5NA 8. MM5CE 9. MM5EC Based on Penta-variate Mixed-Models Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  14. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Methods Nine Methods of Data Normalization 4. MM1NA 5. MM1CE 6. MM1EC Based on Uni-variate Mixed-Models Vector of BLUP Clone x Condition Interaction 7. MM5NA 8. MM5CE 9. MM5EC Based on Penta-variate Mixed-Models Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  15. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Results Observed (RED) vs Expected (BLUE) Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  16. A Quantitative Overview to Gene Expression Profiling in Animal Genetics 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) Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  17. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Results Redundant genes (ie. those with many probes on the array) allow for Validation Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  18. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Results Redundant genes allow for Validation Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  19. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Results 624 Gene Co-Expression (Alphabetical order) Robisomal Proteins Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  20. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Applications Sigrid Brian Keren Siok Kwee Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  21. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Applications False Discovery Rate as a Function of Correlation Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  22. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Applications Callipyge Mutation COL3A1 0.545 UBA52 GNAI2 -0.697 0.584 -0.658 0.602 KARS DLK1 LUM 0.611 -0.639 TNFRSF21 CIDEC 0. 611 DCAL1 Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  23. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Applications Callipyge Mutation 0.754 CAV1 -0.822 DES 0.747 0.853 COL3A1 ACTA1 CTSF 0.767 0.545 UBA52 GNAI2 -0.738 -0.697 FN1 0. 799 0.584 -0.741 -0.658 0.602 KARS DLK1 LUM SPARC 0. 736 0.611 -0.639 TNFRSF21 CIDEC 0.743 TM4SF2 0. 611 DCAL1 0.880 Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  24. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression Applications Callipyge Mutation MYBPC2 0.754 0.883 CAV1 LDHA -0.822 DES 0.889 0.747 0.853 0.889 COL3A1 ACTA1 MYL1 CTSF 0.767 0.545 0.892 UBA52 GNAI2 PGK1 -0.738 -0.697 FN1 0. 799 0.584 0.893 -0.741 -0.658 0.602 KARS DLK1 LUM CASQ1 SPARC 0. 736 0.611 -0.639 TNFRSF21 CIDEC 0.743 TM4SF2 0. 611 DCAL1 0.880 Armidale Animal Breeding Summer Course, UNE, Feb. 2006

  25. A Quantitative Overview to Gene Expression Profiling in Animal Genetics Co-Expression ITM2B PYGM Applications 0.916 -0.899 Callipyge Mutation 0.972 MYBPC2 ENO3 0.754 0.883 0.897 CAV1 LDHA GPI -0.822 DES 0.889 0.747 0.853 0.889 0.910 COL3A1 ACTA1 MYL1 CKM CTSF 0.911 0.767 0.545 0.892 UBA52 GNAI2 PGK1 -0.738 -0.697 FN1 0. 799 0.584 0.893 -0.741 -0.658 0.602 KARS DLK1 LUM CASQ1 SPARC 0. 736 0.611 -0.639 TNFRSF21 CIDEC 0.743 TM4SF2 0. 611 DCAL1 0.880 Armidale Animal Breeding Summer Course, UNE, Feb. 2006

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