Hemiascomycetes Proximity Plots

Hemiascomycetes Proximity Plots

Introduction

To investigate gene order evolution and paleopolyploidy in the hemiascomycetes, our proximity plots display gene order information from 14 species of hemiascomycetes in relation to Saccharomyces cerevisiae. Duplicated genes from S. cerevisiae can also be superimposed on the same plot. Each dot on the plot represent a pair of genes which are linked. By clicking on one of these, the genes can be identified and linkage information from other species is displayed. Clicking on white space constitutes clicking on the nearest dot. Please read our Documentation for more details. Further information regarding the duplicated gene pairs used in this study and the genome coverage of sister regions can be found in the Downloads section.

Please refer to: Wong S., Butler G. and Wolfe K.H. (2002) Gene order evolution and paleopolyploidy in hemiascomycete yeasts.
Proc. Natl. Acad. Sci. USA 99, 9272-9277. [PubMed]

Your browser will require a lot of memory (RAM). We recommend quitting from other applications running on your system before generating a plot.

Configure and generate a proximity plot

Gene pair dots display
Show contig-linked pairs.
Show clone-linked pairs.
Show ambiguous contig-/clone- linked pairs.
Show duplicated gene pairs within S. cerevisiae.

Blocks display

Set 1^* - Show blocks obtained from a combination of gene order information (including ambiguous pairs) and S. cerevisiae duplicated genes information.

Set 2^* - Show blocks obtained from gene order information only.

Set 3 - Show blocks obtained from S. cerevisiae duplicated genes information only (from Seoighe & Wolfe, 1998).

Show areas of genome covered by ...
Highlight overlapping regions between blocks.

Highlight gene:

Partial Plot

You may also generate a partial plot by selecting the chromosomes to be used for the X (left to right) and Y (top to bottom) axes.

Select one or more chromosomes to be used for the X axis

1 2 3 4 5 6 7 8

9 10 11 12 13 14 15 16

Select one or more chromosomes to be used for the Y axis

1 2 3 4 5 6 7 8

9 10 11 12 13 14 15 16

Note: Leaving an axis blank consitutes selection of all 16 chromosomes on that axis

Magnification

Examine the plot more closely by selecting a magnification factor.

(This is only available for partial plots and there is a limit on a plot size of 6000 x 6000 pixels.)

^* These blocks were visually defined with relevant data from 13 species shown above (C. albicans data was excluded).

Downloads

The entire set of S. cerevisiae duplicated gene pairs (one-to-one mutual best hits) - all_dup_pairs.txt
Subset of S. cerevisiae duplicated gene pairs located in blocks^† - block_dup_pairs.txt
Genome coverage of blocks^† in S. cerevisiae - blocks_coverage.txt

^† Blocks obtained from a combination of gene order information (including ambiguous pairs) and S. cerevisiae duplicated genes information (i.e. Set 1, as shown above). They were visually defined with relevant data from 13 hemiascomycete yeasts (C. albicans data was excluded).

Documentation

There will be 3 main windows to help you generate a plot and obtain information from it:

1. Proximity Plot Control Panel

A window will appear containing control boxes similar to those shown above.

[Proximity Plot Control Panel Description]

2. Proximity Plot Main Window (current window)

This shows the plot itself. Clicking on one of the dots will display its supporting evidence in the "Information" window (see below).
Note: Clicking on white space will constitute clicking on the nearest dot.

[Proximity Plot Example]

Hint:
In a full plot, each dot is only 1 pixel in size and they can be difficult to see. Generate a partial plot to examine individual gene pairs or you can use software to magnify part of the screen as follows:

In Windows systems, use the Magnifier (Start -> Programs -> Accessories -> Accessibility -> Magnifier) to examine the plot more closely.
[Have to be installed from the Windows CD in some cases.]
In Macintosh systems, we recommend installing Zoom Lens 2.5.

3. Information Window

This provides supporting evidence of individual dots. The linked pair in question (LYS12 - HDA1) are highlighted in red since they can be within a group of genes which are all either contig- or clone- linked. Contig-linked pairs should appear in the same column of a group table; whereas clone-linked pairs should appear in two adjacent columns. The hyperlinks generate another new window which provides more supporting information.

[Linked Pair Information Window]

Last updated November 2003
Problems or suggestions to swong@tcd.ie