Computational Analysis of Transcript Identification Using GenBank.

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Presentation transcript:

Computational Analysis of Transcript Identification Using GenBank

Differentiation of hematopoietic cells

Genome-wide gene expression

SAGE (Serial Analysis of Gene Expression)

SAGE & GLGI Overview

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

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

Unique Tags among 878,938 EST Derived Tags

Unique Tags among 32,851 Gene Derived Tags

Converting tag into longer 3’ sequence

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

UniGene Human 3’ Part Length Distribution

Number of Tags which Move for k to k+25

Unique Tags among 878,938 EST Derived Tags

Unique Tags among 32,851 Gene Derived Tags

Idealized Construction

Random Model

Ideal Case Tag Count Progression

Myeloid Tag Matches with UniGene Human SAGE Tag Reference Database

SAGE Tag Processing with GIST

k-mer tree

GIST Performance with Improved IO

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