anotation: gene of which little is known what follows is a simulation of an orf page in the proposed...

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 begin:1. Click on Slide Show, (on the upper toolbar)2. Click View Show3. Click Continue button

Continue

Scenario 1

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330

Anabaena PCC 7120: all4312OptionsAnnotateMain Menu History

Replicon: Chromosome

Coordinates: 5166997 (stop) <- 5167767 (start-GTG) System Length = 256 amino acids

Strand: Complementary

Function: Two-component response regulator System Syny6803:sll1330: Expression data (click to expand) Experiment

Mutant: None Syny6803:sll1330: Failed to segregate Experiment

Cyanobacterial orthologs:

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.

Continue

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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).

A

Continue

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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). Continue

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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.Continue

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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.

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330





Function: Two-component response regulator System Syny6803:sll1330: 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



Clicking on the specific experiment gives details concerning protocol and results. Click to contract

the display back to its previous form.

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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 you’ll also need to click.

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330






Mutant: None Syny6803:sll1330: Presumed inviable (failed to segregate) Experiment


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 you’ll also need to click anywhere.

IMP: Masahiko Ikeuchiunpublished

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330






Mutant: None Syny6803:sll1330: Presumed inviable (failed to segregate) Experiment


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.

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








Clicking on the icon would bring your designated e-mail screen with the annotator’s 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 you’ll also need to click anywhere..

Masahiko IkeuchiTokyo University

A

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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.

AABC transporterATP-binding protein

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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.

AResponse receiver domain

(PF00072): 1.4e-31

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330

Anabaena PCC 7120: all4312OptionsOptionsAnnotateMain Menu History







To predict operon structure, it is useful to visualize potential inverted repeats, which may function as

transcriptional termination signals. Operon structure isn’t an issue in this case, but let’s go for it anyway.

Click and then Show inverted repeats.

A

View: graphic

Show cb orthologs

Show hits: <1e-6

Show neighbors: +/- 1

Show motifs

Show alternate starts

Show annotated features

Show predicted features

Show transposon ends

Show tandem repeats

Show inverted repeats

Show dispersed repeats

Show private set


Options

Options

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330

Anabaena PCC 7120: all4312OptionsOptionsAnnotateMain Menu History







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.

A

View: graphic

Show cb orthologs

Show hits: <1e-6

Show neighbors: +/- 1

Show motifs

Show alternate starts

Show annotated features


Show transposon ends

Show tandem repeats


Show dispersed repeats

Show private set


Options

Options

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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

Anab7120:all4312

NostPunc:618.077

TricEryt:5.6053

Syny6803:sll1330

TherElon:tlr1330








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.

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End

Lawrence/Collier conserved motif set

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

Scenario 1

A prototype of the Annotation Page exists in CYORF, but the full capabilities described here

require the resources we are asking of NSF.

anotation: gene of which little is known what follows is a simulation of an orf page in the proposed...

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