Expression Mural

1
Expression Mural
Visualizing Microarray Gene Expression Data
Matt Clement, Margaret Ellis, Josh Steele, Yuying
Tian
Department of Computer Science, Virginia Tech
2
Introduction
3
Data Files
extract
parse
4
Data Files

• number of chromosomes 16
• largest chromosome 1,531,929 base pairs
• length of sequences 300 4,000 base pairs
• sequences per experiment 5,000 10,000
• data fields per experiment 70

5
Data Structure
sequences
chromosome
tier array
X1
X2
X4
X8
6
Hurdles

• Domain knowledge
• Data Management
• Each pixel represents many base pairs
• 260 - 14,000 bp/pixel
• Calculating average ratios
• average(0.2, 5.0) 1
• Gene sequence overlapping
• Java inexperience

7
Future Work

• Mouse over
• Bounding
• boxes
• Rearrange
• order
• Link to more
• information
• Usability
• testing
• Histograms
• Generic input

8
Acknowledgments
Computer Science Department Dr. Chris North Dr.
Lenwood Heath Dr. Craig Struble Virginia
Bioinformatics Institute Dr. Jennifer Weller Dr.
Allan W. Dickerman Virginia-Maryland Regional
College of Veterinary Medicine Dr. Stephen M.
Boyle