Exercise: Use of gene expression data

Finding up-regulated genes using the Stanford Micro-array Database

Go to the Stanford Microarray Database and click on "public search"

Click on advanced results search

Select organism: Homo sapiens, Select Experimenter: All, Category: Chronic Lymphomatic Leukemia, Sub category: All, and then click on display data.

Click on the View and Sort Array Data symbol in the Options column in the first row.

Select Accession and Gene name in the Display box (Clone ID, Gene Symbol, ...) (hold down "CTRL" when selecting the second), and then press "Display".

Try to find out what the different columns mean.
Use the name table to find the variable name (column one in the table) corresponding to the column name in the array data table and look it up in the SMD Schema specifications

Are all the over-expressed genes highly expressed?

open Pubmed in a new window, select: Search "nucleotide". Paste in the accession name for the top entry in the micro-array data table and press "Go".

Click on the entry and mark the sequence with the mouse.

open Nucleotide blast search in a new window, paste in the sequence and press "Blast".

Press format

Click on the 3 top scoring hits

From the function (click on the pubmed link) of these 3 top scoring hits, can you derive what is the function of the protein?

Select the amino acid sequence with the mouse

open BIMAS in a new window, select HLA type A_0201 and paste in the sequence.

How many potential HLA-A*0201 epitopes do you find (Score > 100)?
What are the pros and cons of using these epitopes in a cancer vaccine?

Other uses of expression data

• Look for clusters of genes in immune cells
• Look for clusters of genes in infected cells/cells from infected persons
• Look for up-regulated genes in cancers cells

Links

Introduction to DNA arrays

Chip producers

Micro array databases

Online analysis of DNA array data

Microarray Gene Expression Data Society - MGED Society

Software for DNA array analysis