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LU4: Bioinformatics Tools for Functional Data Analysis (ArrayVision (Data…
LU4: Bioinformatics Tools for Functional Data Analysis
Role of Bioinformatics in Functional Genomics
Providing reference database
Expression database (Array Express, Geo, etc.)
Computational data mining and data analysis via high-throughput analytical software/programs
Example
: Data Mining Analysis (via Gridded DNA/gene arrays)
Biological information (RNA/DNA) is spotted on a solid platform (Chip-based technology) -
microarray chip
Involves:
Image capture and documentation
Conversion of physical image to digital data
Analysis of data
Gene arrays:
High throughput information coding and retrieval platform for gene activities
ArrayVision
Has
basic analysis
,
data reporting
, and
chart/statistics functions
Data mining via ArrayVision
Variation in spot size
spots are
not always
regular shape and size
a
fixed
size element may caused
underestimation of actual signals
segmentation
is required to adjust size of elements to fit individual spot size
template elements
adjust themselves to find the spot boundaries
Detritus removal and background check
detritus
- small components that vary materially from the surrounding pixel values; small point artifacts result from dust; errant bits of labelled target
detritus
"pulls" spot intensity measurement
away
from the optimal spot location
background
- inherent intensities (not due to probe-target hybridization) that surround a spot
all array softwares must allow
substraction
of background reading from spot reading
failure
to remove background readings will cause
false representation of intensities
Alignment
generates a
set of circles, rectangles, or arbitrary shapes
which
define
where data will be
gathered
from the image
set is called a
data template
in which all elements within it should align with the
hybridisation spots
in performing
template-spot alignment
, a
layout
must be defined first
Quality metrics, data report and display
data
- reported in
tabular form
with each column containing a discrete/specific data characteristics (spot coordinates, spot intensities, normalized spot intensities)
tables
can be saved in various formats, and can be exported directly to Excel or other data analysis softwares
initial analysis usually involves
scatterplot charts
Rapid
and
automated analysis
for array images from different types of array format
A software developed for the
quantification of microarray
and
protein arrays data
GenePix Pro
Has added features
Greater flexibility
for background identification and assessment
Select
features
for
flagging with lasso
(looping) selection
Analyzes irregular features
on the image and performs
circularity metric calculation
for higher quality processing
Navigation window
on the Image tab allows researchers to
zoom in to regions of interest
Higher resolution
for segmentation process
Allows more
focus analysis
Provides
scatterplot chart
of microarray results
Produced by Axon instrument
Another complete standalone image analysis software for microarrays, tissue arrays and cell arrays