1.
Sorry, the graph does not perform properly in FireFox. We have tested them under IE/safari + adobe SVG viewer 3 (ASV3).
In fact, we used javascript engine from ASV3 for stable performance accross platform
2. BACKGROUND
For each of 112 yeast segregants,
6195 genes expression traits were measured using cDNA
microarray; over 3000 SNP markers were genotyped (Brem et al 2002
Yvert et at 2003). Multiple Interval Mapping
was applied to this mapping population to obtain expression QTLs (eQTL). About
5000 QTLs across the genome were declared for about 3000 expression traits.
3.
TERMINOLOGY
1. Open Reading Frames (ORF) in the eQTL intervals are called "pORF" in this
application since they are close to DNA polymorphisms. They are listed after
"mapped onto:" in SVG
2. Those ORFs, whose expression levels were used as traits,
are called "eORF" hereafter. They are called 'trait' in SVG.
4.
BASIC GRAPHIC
SETUP
1. Genes are arranged onto chromosomes according to their
physical position
2. Chromosomes are concatenated, from chromosome A to P, to
form x-axis and y axis.
3. Each small horizontal bar is an eQTL,
4. its y coordinate corresponds to the gene whose expression
was used as trait in QTL mapping (i.e. eORF);
5. its coordinates of start and end position correspond to the
physical boundary of eQTL on the chromosome
5.
BASIC OPERATION
1.
Press ctrl and use
mouse to select and zoom
an area
2.
Press alt and use
mouse to drag the picture
3. Notice the zoom option when right clicking. We can go back
to the original view anytime by choosing "Original View"
4. Checkered background (white and mintcream) indicates
chromosome boundaries in x-axis. It tries to convey the general idea about
number of eQTLs mapped onto a chromosome. Mouse pointer"s current
chromosomal region is indicated at the right upper corner.
5.
Dynamic
annotation information. Place mouse pointer on a QTL, eORF, pORF (and also non-ORF
genes in the eQTL) names will show on the right side of the screen. The legend
will be fixed at that position no matter how the picture is zoomed or moved.
All QTLs of a same eORF will be highlighted as red bars when putting mouse
pointer at any QTL of the eORF.
6. Database Connection. Each gene name can be clicked and you will be led to
annotation for it at http://www.yeastgenome.org/.
It is recommended to right-click the name and to open
the webpage in a new window.
7. Searchable. In the lower left corner, there is box where gene name
can be entered in by keyboard. QTLs for that gene will be marked (a red dot in
the middle of each small QTL bar)
8. It is possible to mark a list gene stored in an external
file (see next section).
6.
ADVANCED
OPERATION
1.
It was noticed in this yeast data, that
trans-acting QTL generally do not contain the transcriptional factors for
eORFs. Thus, the possible biological mechanisms underlying these trans-acting
eQTL should be indirect regulations: transcriptional activity modulation between
genes in similar biological processes, in similar biochemical pathways or in
same protein complexes. Current knowledge of gene interaction network can be
superimposed onto the 2 dimensional eQTL mapping plot to inspect visually the
correspondence between known biological mechanism and QTL detected through
statistical analysis.
2.
Using biochemical pathway as an example,
when indirect regulation do contribute to the formation of eQTLs, it is
expected to find 1) pORF is in a same pathway as its eORF 2) eORFs in a same
pathway have eQTLs at same location. Similar argument can be applied to other
kind of known biological networks.
3.
Available patterns/annotation datasets
include finalNet,
complex GO-slim,
MIPS, two Hybrid, synthetic Lethal, transcriptional Factor, over-Presented GO (this
annotation is generated by wei, using termfinder package), KEGG.
4.
Additional annotation information can be
imported into the SVG as long as the files are in the server or folder of the
SVG file. That is to say, annotation files from your
local disk cannot be applied to the SVG application unless they are
uploaded to the www server or the SVG application and a few other files are
downloaded to your local disk.
5.
Here is an example of operation.
1.
After loading the SVG file, click
"click for more Pattern" and find the purple word "KEGG". Click it to show all eORF-pORF pairs,
which are in a same pathway according to KEGG, as purple dots. Place
mouse cursor on the dot, the eQTLsĦŻ information will be shown on the right side
the screen. The pORF, which is in the same pathway as the eORF, is now tagged
with a purple K and is highlighted.
2.
click clear All to
allow new patterns to be imposed
3.
Type KEGG.MARK in the box at the lower left
corner. You want to first click the box before you can type words in it. QTLs
of genes in a same KEGG path way will be marked out with a same (random) color.
Place the mouse point on the dots, we can find (on the right side of the
screen) the eQTL information, and (in the middle of left side of the screen)
the pathway the eORF belongs to. More formal statistical analysis is needed to
find in each genomic location the over-presented eQTLs from a certain pathway.
However, it is easy to find in the middle portion of chromosome O, there are
many genes from oxidative phosphorylation pathway are mapped to similar genomic
location.
7.
DIFFERENCE WITH
THE SIMPLE EXAMPLE
1. Every eORF (trait gene) in the right panel is linked to a
HTML file in local server, which contains the GeneOntolgy annotation for all
genes in the QTL under mouse pointer.
2. Every pORF in the right panel is linked to its annotation
in Saccharomyces Genome Database. By
default, such a link will lead users to NCBI entries.
3. Annotation information is available in the left hand panel.
Check download tab
for more information. It is easy to incoporate such annotation databases into
SVG.
In the above example, trait genes and genes in QTLs are ordered in the same way: their physical distance in the chromosomes. In this example, however, traits are ordered according to their functional similarity. Trait genes of a similar KEGG pathway are assigned with similar y coordinator. Notice in this setting, a trait gene will be duplicated if it appears in more than one pathway.
