Warping Modes
GenTχWarper operates in
two main modes: template matching mode and aligning datasets
mode. The working mode must be selected
at the start from the WarpMode
menu.
At any time
during the run of GenTχWarper the working mode
can be changed. However, bear in mind that by
switching from one mode to another you will loose the
results obtained in the former one, unless you have
saved them to a file before moving to another
mode.
1) Template Matching Mode Interface
2) Aligning Datasets Mode Interface
As it can be seen above, the
two modes have identical menus and tool bars. All
GenTχWarper options can be
accessed either via the menu items or via the short cut buttons on the tool bar.
Input/Output
GenTχWarper currently
accepts as a valid input excel files and tab-delimited text
files. The top row and the left most column of the input files are
preserved for non-digital information, as for
instance experiment and gene identifiers and
anotations:
.
In both modes, the program can export the results to
excel files or tab-delimited text files. The load, save, reset and exit
functions are accessible via the File menu or via the
tool bar buttons:
.
Data Adjustment
In both modes the performance of
the core alignment algorithm is subject to
modification via several parameters: data adjustment,
metric, offset, and anchor point. The data adjustment
option enables z- and log2-transformations to be
performed on the input expression profiles before
alignment. They can be activated via the
Data Adjustment menu or via the buttons:
.
The z-transformation can
be relevant when the general shape rather than the
individual gene expression amplitudes at the
different time points is important. The expression
value of each gene i at any time point
t is adjusted by substructing the mean and
dividing with the standard deviation of the
expression values of gene i over all the time
points. However,
this transformation should be used with caution,
bearing in mind that the expression levels of low
expressed genes will be amplified by it. The
log2-transformation involves normalization of the expression
value of each gene i at any time point
t with the expression value of the same gene
i at time point zero and then taking log2 of
the ratio. This transformation may be
essential for performing between experiment or
between spicies comparisions of gene expression time
series.
Metric
The Metric
menu allows a flexible choice between 3
different distance measures: Manhattan, Euclidean,
Chebychev and Pearson correlation. Alternatively, the desired distance measure can
be selected via the buttons:
.
Warping Window
The Warp Window
menu enables the application of a warping window constraint
during the calculation of the DTW distance. It leads
to a reduction of the search space and
consequently speeds up the processing of large
microarray data sets. The warping window can
alternatively be activated via the button:
.
The size of the warping
window must be given in a pop-up window
indicating the allowed lower and upper
boundaries.
.
Any integer value within the specified range is
accepted as a valid window size. For instance, a size 1
will mean that the optimal alignment path is allowed
to deviate maximum one position to the left or to the
right from the diagonal. The narrower the warping
window is, the faster the final alignment will be
produced. Additionally, the side effect of the
application of a narrow warping window is that the
optimal alignment path will be forced to stay close
to the diagonal. The extreme usage of the warping window feature however,
may have a negative effect on the accuracy of the
alignment.
Offset
The Offset menu enables
specifing a non-zero value as an offset
parameter. This allows to slide the sets of
expression profiles against each other along the
time axis and in this way discovering genes with
similar trajectories but shifted in time. For
instance, putative targets of a known transcription
factor can be identified by using its profile as a
template in the template matching mode and
evaluating the list of the best matching genes for
different offset values. Additionally, the offset
parameter can be useful in case the biological
process under study displays a phase shift due to
the design of the experiment. Note that the offset
option can equivalently be accessed via the buttons:
.
The left button is on-off
switch, while the right one allows setting a new offset
value in the window below. Any integer value
is accepted as a valid offset. For instance, an
offset 2 will mean that the blue profiles are shifted
with 2 time points to the right. Analogously, a negative offset
will cause respective shift to the right of the
red profiles.
.
Anchor Point
The anchor point option provides
the possibility to explicitly fix together a pair of
time points coming respectively from the two sets
of expression profiles to be aligned. Setting an anchor point might be very useful
in case there is detailed information about the
exact times when the compared biological processes
go through some fixed state. This feature is also
useful when one of the time series to be compared is
sampled during a shorter time interval than the
other. Presently only one anchor point can
be specified in GenTχWarper via the Anchor
menu or alternatively via:
.
The left button is on-off
switch, while the right one allows setting the
coordinates of an anchor point in two sequential windows. In the first window,
the index of the time point from the blue profiles to be anchored must be specified:
.
In the second one, the
corresponding index for the red profiles needs to be
supplied. Clearly, only positive integer values
within the time index range of the time series are
allowed as valid anchor point coordinates.
.
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