Biol 591 
Introduction to Bioinformatics
Scenarios
Fall 2002 
Identification of different classes of acute leukemia

Scientific story (html)

In brief: You have in hand RNA from bone marrow samples from two classes of patients: those with acute lymphoblastic leukemia and those with acute myeloid leukemia. Superficially, the two classes of leukemia are very similar, but effective treatment of them differs markedly. How can you use the RNA to identify genes that are expressed differentially between the two classes of leukemia. How can you use this knowledge to build a tool to identify patients with one class or another, thereby pointing the way to effective treatment?
Bioinformatic tools
Statistical analysis of microarray data
     Homegrown program to illustrate simple statistical procedures to identify differentially expressed genes.
Presentations
General statistical considerations - Monday 28 October 2002 (ppt)
Discussion of Golub et al - Wednesday 30 October 2002 (ppt)
Paper: Golub et al (1999). Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring

Data

Expression pattern of 6817 human genes in leukemia patients with identified class of leukemia (txt)
Samples 1 - 27 are from patients with acute lymphoblastic leukemia (ALL)
Samples 28-38 are from patients with acute myeloid leukemia (AML)
Expression pattern of 6817 human genes in leukemia patients with identified class of leukemia (txt)
Samples 39-72 are from patients with acute leukemia of an unknown class
See also web site for paper: http://www-genome.wi.mit.edu/MPR
Perl focus: Planning and writing a Perl program

Problem Set:

Problem Set 6 (part 1): Programming (html)
Problem Set 6 (part 2): Statistical considerations (pdf)