Anotation: Gene of which little is known

1
Scenario 1
Anotation Gene of which little is known
What follows is a simulation of an orf page in
the proposed graphical interface. The interface
does not yet exist. 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 begin1. Click on Slide Show, (on the upper
toolbar)2. Click View Show3. Click Continue
button
Continue
2
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
This is an example of an orf that has only
automated annotation, except for annotation
carried over automatically from its ortholog in
Synechocystis PCC 6803. The notation System
indicates that the assertion has not been
confirmed by a human annotator. Clicking on
System brings you to a page that provides the
basis for the assertion.
Syny6803sll1330
TherElontlr1330
Continue
3
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Clicking on Chromosome brings you to a zoomable
map of the chromosome showing the position of
all4312 (see the more interesting case in
Scenario 5).
Syny6803sll1330
TherElontlr1330
Continue
4
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
Clicking on the coordinates 5166997... brings you
to a view of the sequence of the region around
all4312 (this is the subject of Scenario 6).
TherElontlr1330
Continue
5
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
Clicking on the length 256 amino acids brings you
to the amino acid sequence. Both the DNA and
amino acid sequences can be downloaded in this
way.
TherElontlr1330
Continue
6
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
There is no experimental data (or any other human
annotation) available for all4312. However, there
is microarray data available for its ortholog
sll1330. Click to show these experiments.
TherElontlr1330
7
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
contract) Experiment Suzuki et al
(2001) Cold shock response Experiment
Hihara et al (2001) low light to high
light Experiment Yoshimura et al (2001)
cAMP receptor mutant Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Clicking on the specific experiment gives details
concerning protocol and results. Click to
contract the display back to its previous form.
Syny6803sll1330
TherElontlr1330
8
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
A mutant exists for the ortholog in
Synechocystis. Mouse over to Experiment to see
who made the mutant and whether the work is
published. In real life, information will pop
up when you mouse to an informative position. In
this simulation youll also need to click.
TherElontlr1330
9
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Presumed inviable (failed to
segregate) Experiment Cyanobacterial orthologs

IMP Masahiko Ikeuchiunpublished
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
IMP (Inferred from Mutant Phenotype) is a
standard Gene Ontology Consortium descriptor,
useful for searching (see Scenario 3 for more).
Mouse away from the region. In real life,
information will go away when you mouse away from
an informative position. In this simulation
youll also need to click anywhere.
Syny6803sll1330
TherElontlr1330
10
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Presumed inviable (failed to
segregate) Experiment Cyanobacterial orthologs

A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Clicking on Experiment would bring you to a page
describing the experiment and its results. For
now, mouse over to the Annotator icon to see who
made this annotation. Remember that in this
simulation you have to click to pop up
information over a region.
Syny6803sll1330
TherElontlr1330
11
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
Masahiko IkeuchiTokyo University
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
Clicking on the icon would bring your designated
e-mail screen with the annotators e-mail address
ready to go. For now, mouse away from the
region. In real life, information will go
away when you mouse away from an informative
position. In this simulation youll also need to
click anywhere..
TherElontlr1330
12
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
The bottom part of the screen shows the genetic
neighborhood of all4312 and its cyanobacterial
orthologs. Orfs are color-coded by function.
Mouse over to the gene downstream from all4312
to see its identity. Then mouse away.
Remember to click to view the popup and click
to make it disappear.
ABC transporterATP-binding protein
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
TherElontlr1330
13
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
Mouse over to the red motif bar to see the
identity of the motif found in the indicated
region of all4312. The Pfam number and E-value of
the match are given. Mouse away from the motif
bar. Remember to click to view the popup and
click to make it disappear.
Response receiver domain (PF00072) 1.4e-31
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
TherElontlr1330
14
Options
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
To predict operon structure, it is useful to
visualize potential inverted repeats, which may
function as transcriptional termination signals.
Operon structure isnt an issue in this case, but
lets go for it anyway. Click
and then Show inverted repeats.
Options
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
TherElontlr1330
15
Options
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
There are evidently no features annotated yet for
this orf, but there may be some that have been
automatically predicted. Click
and then Show predicted features.
Options
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
TherElontlr1330
16
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
Surprisingly, the same feature has been predicted
for the entire set of orthologs. Mouse over to
the feature upstream from all4312 to identify it.
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
TherElontlr1330
17
Main Menu
Options
Annotate
History
Anabaena PCC 7120 all4312
Replicon Chromosome Coordinates 5166997 (stop)
lt- 5167767 (start-GTG) System Length 256
amino acids Strand Complementary Function
Two-component response regulator System
Syny6803sll1330 Expression data (click to
expand) Experiment Mutant None
Syny6803sll1330 Failed to segregate
Experiment Cyanobacterial orthologs
Clicking on the green triangle would lead to a
page that describes the motif and how it was
identified. Participant Jackie Collier and Chip
Lawrence are developing a method to predict
transcriptional binding sites. While the set does
not yet exist, the triangles below represent
sites that have actually been identified by a
means similar to that described in Scenario 5.
Lawrence/Collier conserved motif set
A
Anab7120all4312
NostPunc618.077
TricEryt5.6053
Syny6803sll1330
TherElontlr1330
End
18
Scenario 1
Anotation Gene of which little is knownSummary

• The Annotation Page provides links to different
  views of the region surrounding the gene
• The page links to other pages that facilitate
  downloading sequences
• The page provides experimental data when
  available regarding the orf and its
  cyanobacterial orthologs
• DNA features can be visualized wthin the context
  of the genetic neighborhood of the orf

A prototype of the Annotation Page exists in
CYORF, but the full capabilities described here
require the resources we are asking of NSF.