1. Gene expression informatics – it’s all in your mine
Douglas E. Basset Jr, Michael B. Eisen, & Mark S. Boguski
Nature Genetics Supplement, 1999

2. Review of how it works
From SHARING GENE EXPRESSION DATA: AN ARRAY OF OPTIONS
By Daniel Geschwind

3. Steps and Data Lab Information Image Analysis
Turn image (spots) into numerical representation (ratios, usually)
Problem
No standard procedure of software
Variation

4. Steps and Data (continued)
Normalization
Raw numbers normalized to reduce systemic biases (dye absorption rate, mRNA quantities,etc.)
Problem –
Lose information
Various methods of normalization produce differing results

5. Data Integration and Warehousing
Goal – Genbank model
Objective, natural measure of gene expression
Highly curated database
Controlled by rich ontologies
Synergistically hyperlinked to important references

6. Is this goal possible with expression data?
No natural objective unit of measure (like AGCT)
As many entries as cell types X conditions
Lacking standards (since 1999 some standards have been worked on)
Problems of normalizing, especially cross experiment