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Slide #1. Permissions Statement Slide #2. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #3. [IHGSC, Nature 409, 2001] <BR>[Venter et al. Science 29, 2001] Slide #4. The 2 major post-genomic challenges Slide #5. The 2 major post-genomic challenges Slide #6. The 2 major post-genomic challenges Slide #7. The 2 major post-genomic challenges Slide #8. Dark Matter of the Genome Slide #9. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #10. Pseudogenes are among the most interesting intergenic elements Slide #11. Pseudogenes (yG) as Disabled Homologies Slide #12. Duplicated Pseudogenes Slide #13. Retro-pseudogenes (Processed ?G ) Slide #14. Why Study Pseudogenes? Slide #15. Why Study Pseudogenes? Slide #16. Why Study Pseudogenes? Slide #17. Number of Genes and ?G in Slide #18. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #19. Gene Annotations Slide #20. Pseudogene.org : Slide #21. Complexities in yG Calculations Slide #22. Overall Numbers of yG Slide #23. Human Pseudogenes by 3 groups Slide #24. Different criteria for pseudogenes: Slide #25. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #26. Genes vs. Pseudogenes 3:1 Slide #27. Random “Bombardment” of Pseudogenes in the Human Genome Slide #28. Isochore Organization of the Human Genome Slide #29. Repetitive Elements in the Human Genome Slide #30. Distribution of Repeats Among Isochores Slide #31. Distribution of Repeats Among Isochores Slide #32. Distribution of ?genes Among Isochores Slide #33. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #34. The Synteny Between Mouse and Man Slide #35. Human-Mouse Synteny Analysis Slide #36. Age Profile of the ?genes and Repeats Slide #37. Age Profile of the ?genes and Repeats Slide #38. Age Profile of the ?genes and Repeats Slide #39. Human Slide #40. Human Slide #41. Human Slide #42. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #43. Protein Functional Categories of Human Pseudogenes Slide #44. Human & mouse pseudo-genes have a similar distribution amongst functions Slide #45. Genes that have multiple pseudogenes in human also have many pseudogenes in mouse Slide #46. Properties of Genes that Have Multiple ?genes Slide #47. Human Ribosomal Proteins (RP) Slide #48. Human Ribosomal Proteins (RP) Slide #49. Num. RP yG does depend on GC content Slide #50. Cytochrome c: Slide #51. The yG HCP9 is relic of a primordial gene, which still functions in mouse Slide #52. The yG HCP9 is relic of a primordial gene, which still functions in mouse Slide #53. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #54. Mike Snyder (PI) & Sherman Weissman <BR>Tiling of whole chromosomes into small fragments <BR>Large-scale hybridization to find transcribed regions in unbiased fashion and TF binding sites (via ChIP-chip) <BR> Slide #55. Genomic Tiling Arrays Slide #56. Tiling Designer Slide #57. Tiling DB: Slide #58. Analyzes multiple experiments on the same array <BR>Detects and minimizes noise <BR>Assesses data quality <BR>Identifies data elements that are actually differentially hybridized <BR>Provides graphical representations of the analyzed data Slide #59. Approaches for Scoring Oligo-based Tiling Arrays Slide #60. Whole Genome Maskless Array Slide #61. Chromosomal Transcription Slide #62. Tile Transcription of Known Genes and Novel Regions Slide #63. Tile Transcription of Known Genes and Novel Regions Slide #64. Tile Transcription of Known Genes and Novel Regions Slide #65. Earlier Tiling Experiments Focusing Just on chr22: Consistent Message Slide #66. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #67. Chr22: Slide #68. Integration of Different Transcription and Annotation Data on Chr22 Slide #69. Generate an Integrative List of yG for chr 22 Slide #70. Top Functional Families Slide #71. Environmental Response Theme for Duplicated Pseudogenes Slide #72. Distribution of Integrative yG for chr 22 Slide #73. Intersection of Exons with Transcribed Microarray Tiles and other Transcription Evidence Slide #74. Intersection of yG with Transcribed Microarray Tiles and other Transcription Evidence Slide #75. Intersection of yG with Transcribed Microarray Tiles and other Transcription Evidence Slide #76. An Example of Transcribed, Duplicated yG on Cat Eye Syndrome Critical Region Slide #77. Intersection of yG with Microarray Tiles and other Transcription Evidence Slide #78. Intersection of yG with Microarray Tiles and other Transcription Evidence Slide #79. Intersection of yG with Microarray Tiles and other Transcription Evidence Slide #80. Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes Slide #81. Acknow-ledge-ments: Slide #82. Acknow-ledge-ments: Slide #83. Acknow-ledge-ments: Slide #84. Acknow-ledge-ments: Slide #85. Acknow-ledge-ments: Slide #86. Acknow-ledge-ments: