1. Computational Analysis of Transcript Identification Using GenBank Slides by Terry Clark

2. Differentiation of hematopoietic cells

4. Genome-wide gene expression

16. SAGE (Serial Analysis of Gene Expression)

17. Jes Stollberg et al. Genome Res. 2000; 10: 1241-1248 Figure 1 Schematic illustration of the SAGE process

18. SAGE & GLGI Overview

19. What is the chance of duplicate tags? We can assume we are drawing randomly from the set of all 4-letters sequences of the given tag length This is the same problem as having unique overlaps in the contig matching problem for shotgun sequencing

20. Random Model

21. Random model does not reflect biological process Genes evolve by duplication as well as point mutation Many motifs are repeated Function widgets at work? Result is a strong bias in observed biological sequences, not a uniform distribution as the simple model hopes. Here are some numbers ….

22. SAGE tags match to many genes (Tags from Hashimoto S, et al. Blood 94:837, 1999)

23. Tag Frequency Groups for 10-base Tag Set Containing 878,938 Tags for UniGene Human

24. Unique Tags among 878,938 EST Derived Tags

25. Unique Tags among 32,851 Gene Derived Tags

26. Converting tag into longer 3’ sequence

27. Generation of Longer 3'cDNA for Gene Identification (GLGI)

28. UniGene Human 3’ Part Length Distribution

29. Myeloid Tag Matches with UniGene Human SAGE Tag Reference Database

30. SAGE Tag Processing with GIST

31. k-mer tree

33. GIST Performance with Improved IO

34. Conspirators Sanggyu Lee Janet D. Rowley San Ming Wang Terry Clark Andrew Huntwork Josef Jurek L. Ridgway Scott