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Scenario 4
Analysis: Discovery of coregulated genes
What follows is a simulation of the proposed graphical
interface. As you go through the simulation please consider
what capabilities you would want to serve your research and
annotation interests.
A narrative to help you go through the simulation appears in a
red-bordered box, such as the one below.
To begin:
1. Click on Slide Show, (on the upper toolbar)
2. Click View Show
3. Click Continue button
Continue
How do cells control response to light?
What genes are related to the adaptation to high light?
Look for:
• Gene present in Prochlorococcus MED4
MED4 is naturally adapted to grow in high light.
• Ortholog absent in Prochlorococcus MIT9313
MIT9313 is naturally adapted to grow in low light
• Ortholog present in Synechocystis PCC 6803
Reason will become apparent in a moment
• Synechocystis PCC 6803 ortholog responds to high light
Gene turns on by factor > 2 in response to high light
Continue
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Click Build set to start building a new set
Click Display set to see set you or someone else made
Click Set operation to see statements to manipulate sets
Click Variable to give a value to a new or old variable
Data
Click
to access results of experiments
Click Operation to see list of available statements
Click Function to see list of available manipulations
Click any red button to get help
Click Build Set to
begin finding orfs
with the desired
specifications
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Click Set operation to see statements to manipulate sets
Click Variable to give a value to a new or old variable
Data
Click
to access results of experiments
Click Operation to see list of available statements
Click Function to see list of available manipulations
Click any red button to get help
You want to go through
all MED4 ORFS. Click
Operation to see how to
do that.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider X in set... (loop)
IF... THEN... OTHERWISE
Click
Click
to go through each element of a set
IF... THEN... OTHERWISE
to perform actions only under certain
conditions
Click any red button to get help
Consider X in set... (loop)
You want to go consider
each ORF in the set of all
all MED4 ORFS. Click
Consider X in set…
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
Choose ORFs as the set
type and
Prochlorococcus MED4
as the database.
Choose set type
Choose database
All nucleotides of
All open reading frames of
All amino acid sequences of
All intergenic regions of
Human-annotated orfs of
Private set
Public set
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH
Synechocystis PCC 6803
Thermosynechococcus
Trichodesmium
Unicellulular
Filamentous
All
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Choose database
Consider each item in
Choose ORFs as the set
type and
Prochlorococcus MED4
as the database.
All open reading frames of
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH
Synechocystis PCC 6803
Thermosynechococcus
Trichodesmium
Unicellulular
Filamentous
All
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
Click
Click
Click
Click
Click
Variable
Data
Operation
Function
Set operation
All open reading frames of
Prochlorococcus MED4
to give a value to a new or old variable
to access results of experiments
to see list of available statements
to see list of available manipulations
to see statements to manipulate sets
You want to consider this
MED4 ORF only if an
ortholog in MIT9313 doesn’t
exist.. Click Operation and
choose If… then…
:
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
Click
Click
Consider X in set... (loop)
IF... THEN... OTHERWISE
All open reading
frames of
KEEP item
Prochlorococcus MED4
:
to go through each element of a set
IF... THEN... OTHERWISE
to perform actions only under certain
conditions
Keep item
Click
to add item to set
Click any red button to get help
Consider X in set... (loop)
You want to this MED4 ORF
only if an ortholog in
MIT9313 doesn’t exist..
Click Operation and choose
If… then…
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Prochlorococcus MED4
Data
Click Variable
or Function to
begin specifying condition to be met
Your condition is that the
ortholog of the item in
MIT9313 doesn’t exist.
Ortholog of… is a
function.
:
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Your condition is that the
ortholog of the item in
MIT9313 doesn’t exist.
Ortholog of… is a
function.
Ortholog of
Protein product of
All open reading frames of
Prochlorococcus
MED4
Sequence
of
Upstream region of
Downstream region of
:
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
All open reading frames of
Variable
IF
Ortholog of
(
You want the ortholog of
the item (the specific ORF
of MED4 being
considered)…
Item
Set
Specify
Prochlorococcus MED4
Choose database
in
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH8102
Synechocystis PCC 6803
Thermosynechococcus
Trichodesmium
)
:
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
All open reading frames of
Prochlorococcus MED4
Choose database
IF
Ortholog of
(
... And you want the
ortholog of the item in
Prochlorococcus
MIT9313
Item
in
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH8102
Synechocystis PCC 6803
Thermosynechococcus
Trichodesmium
)
:
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
=

exists
All open reading
frames of
doesn’t exist
Item
in
Prochlorococcus MED4
Prochlorococcus MIT9313
:
)
Click specific operation to continue specifying
the condition to be met
or click
Variable
You want the ortholog of
the item in
Prochlorococcus MIT9313
not to exist.
to save results of function
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
AND
OR
All open reading
frames of
BUT NOT
IF... THEN... OTHERWISE
Item
in
Prochlorococcus MED4
Prochlorococcus MIT9313
)
:
doesn’t exist
Click a logical operation to continue specifying
the condition to be met
or IF... THEN... to end the condition
Let’s pause to see where we
are in the task at hand
(Click to proceed)
How do cells control response to light?
What genes are related to the adaptation to high light?
Look for:
√
√
• Gene present in Prochlorococcus MED4
MED4 is naturally adapted to grow in high light.
• Ortholog absent in Prochlorococcus MIT9313
MIT9313 is naturally adapted to grow in low light
• Ortholog present in Synechocystis PCC 6803
Reason will become apparent in a moment
• Synechocystis PCC 6803 ortholog responds to high light
Gene turns on by factor > 2 in response to high light
Continue
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
AND
OR
All open reading
frames of
BUT NOT
IF... THEN... OTHERWISE
Item
in
Prochlorococcus MED4
Prochlorococcus MIT9313
)
:
doesn’t exist
Click a logical operation to continue specifying
the condition to be met
or IF... THEN... to end the condition
There are more conditions to
fulfill, so click AND.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
All open reading frames of
Item
in
Prochlorococcus MED4
Prochlorococcus MIT9313
)
Data
Click Variable
or Function to
continue specifying condition to be met
Your condition now is
that the ortholog of the
item in Synechocystis
does exist. Ortholog of…
is a function.
:
doesn’t exist
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
Your condition now is
that the ortholog of the
item in Synechocystis
does exist. Ortholog of…
is a function.
Ortholog of
Protein product of
All open reading frames of
Prochlorococcus
MED4
:
Sequence
of
Upstream region of
Downstream
region of
Item
MIT9313
in Prochlorococcus
) doesn’t exist
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
All open reading frames of
Item
in
Variable
Ortholog of
(
You want the ortholog of
the item (the specific ORF
of MED4 being
considered)…
Item
Set
Specify
Prochlorococcus MED4
doesn’t exist
Prochlorococcus MIT9313
Choose database
in
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH8102
Synechocystis PCC 6803
Thermosynechococcus
Trichodesmium
:
)
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
All open reading frames of
Item
in
Prochlorococcus MED4
doesn’t exist
Prochlorococcus MIT9313
Choose database
Ortholog of
(
You want the ortholog of
the item in
Synechocystis PCC 6803
Item
in
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH8102
Synechocystis PCC
PCC6803
Synechocystis
6803
Thermosynechococcus
Trichodesmium
:
)
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
=

exists
All open reading
frames of
doesn’t exist
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
:
doesn’t exist
)
Click specific operation to continue specifying
the condition to be met
or click
Variable
You want the ortholog of
the item in Synechocystis
PCC 6803, this time to
exist... but first you need to
save the ortholog for later.
To do this click Variable.
to save results of function
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
doesn’t exist
)
Type variable name
(assigned to
6803 ortholog
:
)
Give the ortholog a logical
name so that you can refer to
it later (for now, just click on
the box and I’ll do the
typing)
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
=

existsframes of
All open reading
doesn’t exist
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
6803 ortholog
:
doesn’t exist
)
)
Click specific operation to continue specifying
the condition to be met
or click
Variable
Now you can demand that
the ortholog of the item in
Synechocystis PCC 6803
exists.
to save results of function
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
AND
OR
All open reading
frames of
BUT NOT
IF... THEN... OTHERWISE
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
6803 ortholog
:
doesn’t exist
)
exists
)
Click a logical operation to continue specifying
the condition to be met
or IF... THEN... to end the condition
Still one more condition
(2x expression) so click
AND.
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
6803 ortholog
)
)
Data
Click Variable
or Function to
continue specifying condition to be met
This time the condition to
be met concerns data from
a microarray experiment.
Click Data.
:
doesn’t exist
AND
exists
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
6803 ortholog
Variable
data for
Item
6803 ortholog
Specify
)
:
doesn’t exist
AND
exists
AND
)
Choose organism used
in
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
The data desired concerns
Prochlorococcus S120
Synechococcus PCC6301 the 6803 ortholog and an
Synechococcus PCC7942
experiment using
Synechococcus WH8102
Synechocystis PCC6803
Synechocystis PCC 6803
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
6803 ortholog
)
:
doesn’t exist
AND
exists
AND
)
Choose organism used
data for
6803 ortholog
in
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
The data desired concerns
Prochlorococcus S120
Synechococcus PCC6301 the 6803 ortholog and an
Synechococcus PCC7942
experiment using
Synechococcus WH8102
Synechocystis PCC6803
Synechocystis PCC 6803
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
6803 ortholog
doesn’t exist
AND
exists
AND
)
)
Choose type
data for
6803 ortholog
It’s a microarray
experiment…
in
Synechocystis PCC 6803
:
microarray
2D gel
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Prochlorococcus MED4
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
6803 ortholog
)
)
:
doesn’t exist
AND
exists
AND
High light vs low
light experiment
Choose expt
data for
6803 ortholog
It’s a microarray experiment,
Hihara et al, you think…
Mouse over that experiment
to see (here click on it)
in
Synechocystis PCC 6803
microarray
Hihara1
Suzuki1
Yoshimura1
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
Ortholog of
(
Ortholog of
(
<
< or =
= frames of
All open reading
Prochlorococcus MED4
:

> or =
doesn’t exist
Item
in> Prochlorococcus MIT9313
exists
doesn’t exist
Item
Synechocystis PCC 6803
in
exists
)
(assigned to
data for
6803 ortholog
6803 ortholog
in
)
Synechocystis PCC 6803
microarray
Hihara1
You want the
experimental condition
(high light) to be greater
than the control…
AND
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
All open reading frames of
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
data for
6803 ortholog
6803 ortholog
in
:
Prochlorococcus MED4
)
doesn’t exist
AND
exists
AND
)
Synechocystis PCC 6803
microarray
Hihara1
Value
>
+2
You want the
experimental condition
(high light) to be greater
than the control by a
factor of 2 (I’ll type it).
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
AND
OR
All open reading
frames of
BUT NOT
IF... THEN... OTHERWISE
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
data for
6803 ortholog
6803 ortholog
in
:
Prochlorococcus MED4
)
doesn’t exist
AND
exists
AND
)
Synechocystis PCC 6803
microarray
Hihara1
Value
>
+2
Click a logical operation to continue specifying
the condition to be met
(Let’s pause again)
or IF... THEN... to end the condition
How do cells control response to light?
What genes are related to the adaptation to high light?
Look for:
√
√
√
√
• Gene present in Prochlorococcus MED4
MED4 is naturally adapted to grow in high light.
• Ortholog absent in Prochlorococcus MIT9313
MIT9313 is naturally adapted to grow in low light
• Ortholog present in Synechocystis PCC 6803
Reason will become apparent in a moment
• Synechocystis PCC 6803 ortholog responds to high light
Gene turns on by factor > 2 in response to high light
Continue
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Consider each item in
IF
AND
OR
All open reading
frames of
BUT NOT
IF...
IF... THEN...
THEN... OTHERWISE
OTHERWISE
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
data for
6803 ortholog
6803 ortholog
in
:
Prochlorococcus MED4
)
doesn’t exist
AND
exists
AND
)
Synechocystis PCC 6803
microarray
Hihara1
Value
>
+2
That’s it! We’ve specified all
the conditions, so end the IF
segment and specify what do
do if all the conditions are
met.
Click a logical operation to continue specifying
the condition to be met
or IF... THEN... to end the condition
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
IF
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
data for
6803 ortholog
>
Click
Click
Click
Click
Click
Variable
Data
Operation
Function
Set operation
+2
6803 ortholog
in
)
doesn’t exist
AND
exists
AND
)
Synechocystis PCC 6803
microarray
Hihara1
THEN
to give a value to a new or old variable
to access results of experiments
And if they are met, what
you want to do is to save the
to see list of available statements
gene in the set you’re
building, a Set operation.
to see list of available manipulations
to see statements to manipulate sets
Build set
Display set
Variable
IF
Data
Ortholog of
(
Ortholog of
(
in
Item
+2
Cancel
Done
)
doesn’t exist
AND
exists
AND
)
Synechocystis PCC 6803
THEN
In other words, you want to
ADD the gene to the growing
set.
Synechocystis PCC 6803
6803 ortholog
in
6803 ortholog
>
HELP
ADD TO
Operation
Function
DELETE
FROM
UNION OF
INTERSECTION OF
Item
in Prochlorococcus MIT9313
Arithmetic
(assigned to
data for
Set operation
microarray
Hihara1
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
IF
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
data for
6803 ortholog
>
+2
Item
6803 ortholog
Specify
exists
AND
Synechocystis PCC 6803
microarray
THEN
Variable
Add
AND
)
6803 ortholog
in
)
doesn’t exist
Type name of set
to
Which gene? I could save
the Prochlorococcus gene
(the item), but I’ll instead
save the gene from PCC
6803 (more known about
them).
Hihara1
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
IF
Ortholog of
(
Item
in
Prochlorococcus MIT9313
Ortholog of
(
Item
in
Synechocystis PCC 6803
(assigned to
data for
in
6803 ortholog
>
+2
6803 ortholog
Synechocystis PCC 6803
THEN
6803 ortholog
I need to give the set a logical
name (you click, I’ll type).
to
AND
exists
AND
)
Type name of set
Add
)
doesn’t exist
Light-specific genes
microarray
Hihara1
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
(
Ortholog of
(assigned to
data for
6803 ortholog
>
in
Item
+2
Synechocystis PCC 6803
6803 ortholog
in
)
exists
)
Synechocystis PCC 6803
microarray
Hihara1
THEN
Type name of set
Add
Click
Click
Click
Click
Click
6803 ortholog
Variable
Data
Operation
Function
Set operation
to
Light-specific genes
to give a value to a new orIf Iold
variable
stop here, then all
Prochlorococcus genes will
to access results of experiments
be considered, and if the
to see list of available statements
conditions are met, the 6803
ortholog will be saved.
to see list of available manipulations
That’s what I want, so click
to see statements to manipulateDone.
sets
AND
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
(
Ortholog of
(assigned to
data for
+2
Synechocystis PCC 6803
6803 ortholog
in
6803 ortholog
>
in
Item
)
Synechocystis PCC 6803
THEN
Type name of set
Add
6803 ortholog
That was a complicated
script, so I’ll save it in case I
(or someone else) needs to
run it again or modify it.
to
Save
Save results
results and
and script
script
Save only results
exists
)
AND
Light-specific genes
microarray
Hihara1
Equivalent script that bypasses interface
(loop for item in (#^Genes ProcMed4)
as all-orthologous =
(all-blast-orthologous-geneIDs item stdevalue)
as 6803ortholog = (#^Genes Syny6803) :in all-orthologous)
as light-specific-genes = nil
when (and (there-are-not-any #’member-geneID-of-gene-frames
(#^Genes slotv Proc9313) :in all-orthologous))
(there-are-any #'member-geneID-of-gene-frames
6803ortholog)
(>= ratio-value (select-matching-geneIDs-from-table
Hihara1 item) 2))))
collect light-specific-genes 6803ortholog)
This is the script that the interface would
have produced. It looks for all the world
like a computer program. In fact, it is a
computer program, written in BioLingua.
Continue
Build set
Display set
Set operation
HELP
Set: Light-specific genes
Syny6803:sll0990
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
Here are the results of the
program. The genes meeting all
the conditions are given along
with a brief description and a
graphic display of the regions
surrounding the genes.
(Click to proceed)
Done
Build set
Display set
Set operation
HELP
Done
Set: Light-specific genes
Syny6803:sll0990
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
What can you do with this set?
Certainly one thing of interest is
the function of the genes.
Clicking on a gene name brings
you to the annotation page. Try
clicking on slr1332.
Main Menu
Annotate
Options
History
HELP
Synechocystis PCC 6803: slr1332
Replicon: Chromosome
Coordinates: 1670650 (start-ATG)
Length = 404 amino acids
1671864 (stop)
Human
A
Human
A
Experiment
A
Strand: Direct
Gene name(s): fabF or fabJ
Function: beta-ketoacyl-acyl carrier protein synthase
Activity:
In vivo activity: exists
Cyanobacterial orthologs:
Syny6803
Nost7120
NostPun
More
You can find out more
about this kind of page
from Scenarios 1 – 3.
For now, click to return
to the Set Display page.
Build set
Display set
Set operation
HELP
Set: Light-specific genes
Syny6803:sll0990
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
Another interesting point of attack is the
regulation of this set of genes (after all,
they were selected as being coregulated
by light). Perhaps the upstream regions
share a common motif.
(Click to continue)
Done
Build set
Display set
Set operation
HELP
Set: Light-specific genes
Syny6803:sll0990
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
Unfortunately, in three cases, the genes
don’t have an upstream region. Evidently
these genes are part of operons. We’d
like to consider the upstream regions of
the operons by adding the first genes of
the operon to the set. Add to set... that’s a
Set operation. (Click on that)
Done
Build set
Display set
Set operation
HELP
Done
ADD TO
Operation
Set: Light-specific
DELETE
FROM genes
UNION OF
Syny6803:sll0990
Formaldehyde dehydrogenase (glutathione dependent)
INTERSECTION OF
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Arithmetic
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
Click ADD TO...
Build set
Display set
Set operation
HELP
Done
Set: Light-specific genes
Syny6803:sll0990
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
Add to set
Find specific gene
Add set of genes
Specify gene
Click on icon of gene
Click ADD TO and click
on the icon (the short black
arrow) upstream from
sll0990, the first gene
without an upstream
region.
Build set
Display set
Set operation
HELP
Done
Set: Light-specific genes
Syny6803:sll0990
Syny6803:srl7009
Formaldehyde dehydrogenase (glutathione dependent)
trnR: tRNA Arg (UCU)
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
Add to set
Find specific gene
Add set of genes
Specify gene
Click on icon of gene
The short arrow is now
named and part of the set.
Click on the icon (the long
black arrow) upstream
from slr1332, the next gene
without an upstream
region.
Build set
Display set
Set operation
HELP
Done
Set: Light-specific genes
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:srl7009 trnR tRNA Arg (UCU)
Syny6803:sll0990
Syny6803:slr1331
Processing protease
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0576
Putative epimerase/hydratase
Add to set
Find specific gene
Add set of genes
Specify gene
Click on icon of gene
slr1331 is now part of the
set. Click on the icon
upstream from sll0789, the
third gene without an
upstream region.
Build set
Display set
Set operation
HELP
Set: Light-specific genes
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:srl7009 trnR tRNA Arg (UCU)
Syny6803:sll0990
Syny6803:slr1331
Processing protease
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0788
Hypothetical protein
Syny6803:sll0576
Putative epimerase/hydratase
Add to set
Find specific gene
Add set of genes
Specify gene
Now the genes presumably at the
start of the operons have been
Click on icon of gene
added, and it’s time to remove the
genes without upstream regions.
Click on the radio buttons of the
three genes and click Set operation.
Done
Build set
Display set
Set operation
HELP
KEEP (delete others)
Set: Light-specific
DELETE FROM genes
Formaldehyde dehydrogenase (glutathione dependent)
Syny6803:srl7009 trnR tRNA Arg (UCU)
Syny6803:sll0990
Syny6803:slr1331
Processing protease
Syny6803:slr1332 fabF beta ketoacyl acyl carrier protein synthase
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0789
Response regulator (OmpR)
Syny6803:sll0788
Hypothetical protein
Syny6803:sll0576
Putative epimerase/hydratase
Click DELETE FROM to
remove the three genes
from the set.
Done
Build set
Display set
Set operation
HELP
Done
Set: Light-specific genes
Syny6803:srl7009 trnR tRNA Arg (UCU)
Syny6803:slr1331
Processing protease
Syny6803:sll0337
Sensor histidine kinase
Syny6803:sll0335
Hypothetical
Syny6803:sll0788
Hypothetical protein
Syny6803:sll0576
Putative epimerase/hydratase
Now you have what you want: a
set of genes coregulated by
light. The game now is to
extract their upstream regions
and determine if that set
contains a common sequence
motif. So you need a new set.
Click Build set.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Click Display set to see set you or someone else made
Click Set operation to see statements to manipulate sets
Click Variable to give a value to a new or old variable
Data
Click
to access results of experiments
Click Operation to see list of available statements
Click Function to see list of available manipulations
Click any red button to get help
The set will be based on
the upstream regions of the
set of light-specific genes.
Upstream region of... that’s
a Function.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Ortholog of
Protein product of
Sequence of
Upstream region of
Downstream region of
Common sequences
(Meme) of
The set will be based on
the upstream regions of the
set of light-specific genes.
Upstream region of...
that’s a Function.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Choose variable
(
6803 ortholog
Set
Specify
Choose database
in
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH8102
Synechocystis PCC 6803
Thermosynechococcus
Trichodesmium
)
You want not the upstream
region of a variable (6803
ortholog is the only one
you’ve made so far) but
rather a set.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
(
Choose set type
Choose database
All open reading frames of
Human-annotated orfs of
Private set
Public set
Arthrobacter platensis
Gloeobacter violaceus
Microcystis aeruginosa
Nostoc punctiforme
Nostoc PCC 7120
Prochlorococcus MED4
Prochlorococcus MIT9313
Prochlorococcus S120
Synechococcus PCC6301
Synechococcus PCC7942
Synechococcus WH8102
Synechocystis PCC 6803
Thermosynechococcus
Trichodesmium
)
You have a couple of
premade sets available,
but you want your own.
Click Private set.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Choose set
(
Light-specific genes
Type set name
) assigned to
You’ve made only one set.
Choose it...
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Type set name
Light-specific genes
assigned to
Upstream light-sp genes
You’ve made only one set.
Choose it... and give it a
name (I’ll type it).
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Type variable name
Light-specific genes
assigned to
Upstream light-sp genes
Click Display set to see set you or someone else made
Click Set operation to see statements to manipulate sets
Click Variable to give a value to a new or old variable
Data
Click
to access results of experiments
Click Operation to see list of available statements
Click Function to see list of available manipulations
Click any red button to get help
You want to run this new
set through a filter that will
give you conserved motifs.
That’s a Function.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Light-specific genes
assigned
Ortholog of
Protein product of
to Upstream
Sequence oflight-sp genes
Upstream region of
Downstream region of
Common
Common sequences
sequences
(Meme)
(Meme) of
of
The function you want,
Meme, analyzes a set of
sequences for statistically
overrepresented motifs.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Common
sequences of
Light-specific genes
assigned to
Choose set
Light-specific genes
Upstream light
sp-genes
light-sp
genes
Public set
Premade set
You now have two private
sets. You want, of course,
the set of upstream lightspecific genes.
Upstream light-sp genes
Type variable name
assigned to
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Common
sequences of
Light-specific genes
assigned to
Upstream light-sp genes
Type variable name
Upstream light-sp genes
assigned to
Memed light-sp genes
You click and I’ll type in a
logical name.
Build set
Display set
Set operation
HELP
Cancel
Variable
Data
Operation
Function
Done
Upstream
region of
Common
sequences of
Light-specific genes
assigned to
Upstream light-sp genes
Type variable name
Upstream light-sp genes
assigned to
Memed light-sp genes
Click Display set to see set you or someone else made
Click Set operation to see statements to manipulate sets
Click Variable to give a value to a new or old variable
Data
Click
to access results of experiments
Click Operation to see list of available statements
Click Function to see list of available manipulations
Click Done to put your
Click any red button to get help
plans into action and to
display the last defined
set.
Build set
Display set
Set operation
HELP
Done
Set: Memed upstream light-sp genes
Len
Pos E-val
Upstream of Syny6803:srl7009 638 D 509 6.38e-05
Upstream of Syny6803:slr1331 159 D 152 4.38e-05
Upstream of Syny6803:sll0337
138 D
Upstream of Syny6803:sll0335
279 D 183 5.30e-05
Upstream of Syny6803:sll0788
221 D 184 1.09e-05
Upstream of Syny6803:sll0576
79 D
34 3.29e-05
28 1.31e-04
And there you have it! A conserved
octomeric sequence found in front of
all six light-regulated genes (and,
gratifyingly, all in the same
orientation: Direct rather than
Reverse). Is the sequence involved in
gene regulation? Only experiments
will tell...
Left flank
AAATATGGGA
GGCCCATGGG
AGCTTAAAAA
AAGGGTTAGC
TGCTTTGCCA
TTTTTTGCTT
Motif
GAATGGAA
GACTAGGA
GACTAGAA
GACTGGAG
GACTGGAA
TACTGGGA
Right flank
TTGAGTAGCA
TTCAATGGGT
TTGGCAAAAC
TTAGAGAAGG
ACGGATATTT
What have we done?
• Drawn on complex knowledge base
• Combined multiple tools
• Written a computer program
• Modified set by hand
Did it ourselves
Continue
Scenario 4
Analysis: Discovery of coregulated genes
Summary
• The graphical interface facilitates searches using functions,
loops and Boolean operations, with few of the complexities
of most computer languages
• The graphical interface facilitates the searching through
experimental data for orfs with desired properties
• The script interface permits interaction between the search
and display capabilities of the web site and outside resources.
Reminder: This was a simulation.
The underlying language (BioLingua) exists,
but not the interface that facilitates access.
End