BIOL 210: Application and Analysis of (Biological) Microarrays
Spring Quarter, 2007
Part A - Pseudo Grant (50%)
Write up a 5-8 page pseudo-grant in which you describe a pilot study to
be funded using microarray-based technology. The study should be
be completed within 3-9 months, for a total budget of $35,000 or
less. Your goal is collect enough preliminary data to later be
able to write a full-fledged grant for NIH or NSF funding for 3-5 years
(not part of this assignment).
You may work in groups of two (2) to brainstorm, outline and write-up
your grant. Each person should contribute equally to all parts of
assignment (please make sure both group members carefully proof-read
and edit final submission!)
This pilot grant proposal will include:
A. Brief introduction
(1) biological problem to be studied
(2) technology to be used (why is this an effective
use of this technology? why is it better than a traditional molecular
B. Specific Aim(s) - specifically state what you are trying to do.
For example: To measure
stage-specific changes in host cell/tissue gene expression upon
infection with Salmonella in order to identify
genes involved in
host immunological response.
C. Experimental Plan - Describe how you plan to carry out your array
(1) Array platform, type of probes, approximate cost
(2) Experimental design: how many biological
replicates or time-course samples taken & when, how many technical
replicates, use of dye swaps
(3) Types of postive or negative controls you plan
D. Analysis Plan
(1) What tools/program will you use to analyze your
(2) How will you assess the significance of your new
gene list of interest?
E. Supporting, Follow-up, & Future experiments --
(1) In the best array papers we've read in class,
all have follow-up experiments to support major findings. Propose
at least two types of supporting non-array based experiments that could
be done to increase the confidence in the array findings
(2) If you can think of any computational / genomic
/ proteomic follow-up future studies that could leverage your new
findings, describe them briefly (i.e., identifying new transcription
factor binding sites, pathogenicty islands of genes that could be
targetted for drug development, working out full pathways
using genetic screens, etc).
Part B - Data Analysis from your wet-lab experiments (50%)
A. Apply a grid to your array data (TIFF files), and exract grp files.
B. Normalize your data using an appropriate method covered in class,
show your arrays before and after normalization, comment on any
"blemishes" or other obvious problems pre-normalization, and if the
normalization fixed these problems.
C. Do at least one test for statistical significance of differentially
expressed genes (i.e. SAM, but can use others as well if clearly
If using SAMm, use a 3% false positive rate as cutoff value.
D. Give tables of genes (1) significantly up-reglated in heat-shock (up
to top 30), (2) significantly down-regulated (up to 30 genes).
Are there any unknown or unexpected genes, based on their
annotation? Comment on any trends in annotation -- you can use
genome browser to look at additonal comparative gene information (i.e.
Pfam domains, conservation or lack of, nearby intergenic regions
that have similar expression patterns, etc).
E. Perform average or complete linkage clustering using Pearson
correlation on all genes and arrays (from all groups). Did the
arrays cluster by group,
by dye-swap, or by hyb protocol? Describe at least two clusters
that seems particularly well-defined WRT the annotated genes -- a 1-3
assessment of the biological significance of these clusters. Do
any of these genes appear in the same operon in looking at the genome
browser? (if so,
give several examples).
F. Based on one gene known to be involved in heat shock (hsp20/PF1883)
and at least three others described in this published heat
did the arrays reflect a successful heat shock experiment (albeit very
G. What follow-up experiments would you do to improve your confidence
in your analyses using (1) more array-based experiments, and (2)
non-array based experiments?
Requisite files: GAL file Experiment Details file
Image Scan Data
Aaron & Kivanc Hyb TIFs: C101
Marcos & Daniel Hyb TIFs: C103
Pinal, John & John Hyb TIFs: C105
From Nick: C101
C102 C103 C104 C105 C106
From Grant: C101
Grant, Rachel, & Greg, please use Aaron and Kivanc's hyb
experiments for your own group.
As soon as people have produced .GPR files (by thursday) from gridding
your TIF files, please send them to me so that
I can post them for the other groups to use in their analyses (this
includes Grant's group).