Lab_2-I_Hussmann

Lab_2-I_Hussmann - Jeff
Hussmann
 Lab
2
...

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Unformatted text preview: Jeff
Hussmann
 Lab
2
 2/23/2009
 1. I
moused‐over
'Lists',
then
clicked
'Publications',
then
selected
'Saccharomyces
cerevisiae'
from
 the
'Limit
display'
drop‐down
menu,
then
scrolled
down
to
find
a
link
to
 http://smd.stanford.edu/cgi‐bin/publication/viewPublication.pl?pub_no=90.
 2. The
GO
terms
are
‘Cell
cycle
‐
GO:0007049’
and
‘Response
to
pheromone
‐
GO:0019236’.
 3. There
are
many
more
gene
matches
for
"cell
cycle"
than
for
"response
to
pheromone".
"Cell
 cycle"
returns
data
from
211
biosequence_ids,
while
"response
to
pheromone"
returns
data
 from
32
biosequence_ids.
 Raster
Image
of
Cell
Cycle
Data
 
 Spot
Image
of
Cell
Cycle
Data
 
 Raster
Image
of
Pheromone
Data
 
 Spot
Image
of
Pheromone
Data
 
 There
is
considerably
less
periodicity
(alternation
of
red
and
green)
visible
in
the
response
to
 pheromone
data
than
there
is
in
the
cell
cycle
data.
The
spot
image
data
is
much
harder
to
 visually
interpret
than
the
raster
images.
While
the
periodicity
is
visible
in
the
spot
images
if
the
 raster
images
are
used
as
a
guide
for
where
to
look,
it
would
be
hard
to
spot
unaided.

 4. 
 
 Raster
Image
of
Sorted
Spellman
Data
 
 Spot
Image
of
Spellman
Sorted
Data
 
 The
raster
image
of
the
Spellman
data
has
a
distinct
travelling
wave
appearance.
This
makes
 sense
because
the
genes
are
displayed
in
order
of
the
initial
phase
offset
of
their
expression
 relative
to
the
cell
cycle.

 5. 4397
biosequence_ids
pass
the
filtering
stage.
With
no
gene
filter
on,
6194
biosequence_ids
are
 passed.

 
 Raster
Image
of
Data
for
All
Yeast
Genes
 6. I
first
tried
to
use
GO
term
GO:0043232
:
intracellular
non‐membrane‐bound
organelle.
All
of
 the
data
was
filtered
out.
I
then
tried
to
use
GO:0045449
:
regulation
of
transcription,
and
I
kept
 all
other
settings
the
same.
67
biosequence_ids
from
18
arrays
passed
data
filtering,
and
42
 biosequence_ids
from
18
arrays
passed
gene
filtering.
 Raster
Image
of
Transcription
Regulation
Data
 
 Spot
Image
of
Transcription
Regulation
Data
 7. I
used
Mathematica
to
generate
a
raster
image
for
the
response
to
pheromone
data
from
 question
3.
The
Mathematica
notebook
and
cdt
file
used
are
included.
The
resulting
image
is
 qualitatively
similar
to
that
produced
by
the
SMD
tool.
 
 ...
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This note was uploaded on 01/12/2010 for the course BME 341 taught by Professor Staff during the Fall '08 term at University of Texas.

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