close

Вход

Забыли?

вход по аккаунту

код для вставкиСкачать
Database of Arabidopsis Affymetrix Data
Like NASCArrays
Largely overlapping Dataset
With Data Analysis Toolbox
Also like NASCArrays
…but some different tools
My Colour Code:
What we have to tell tool
What tool can tell us
One gene
another
chips
View expression of
(up to 10) selected genes
on selected arrays
Expression
Alternatively:
view as table of data.
plots the expression of
one gene against that of another gene
on selected arrays.
~= NASC Two-Gene Scatterplot
( Presence Calls:
Also calculated for each gene
by MAS5.
If p-value < 0.05 then considered present.
Roughly correlate to signal value. )
Gene 2 expression
Each spot represents one array
Present in
both genes
Present
in Gene 2
Present
in Gene 1
Present in neither
view annotation by clicking spot.
Gene 1 expression
Gene Atlas, Gene Chronologer and Response Viewer
3 tools to visualise expression profile over a set of…
– Organs
– Developmental stages
– Treatments
Each Organ/Stage/Treatment is the mean of a set of chips.
Each tool can be used for 2 tasks
1) Estimation of
how strongly a chosen gene is expressed over the selected profile
2) To identify genes expressed specifically in
chosen Organs/Stages/Treatments
and not at other chosen Organs/Stages/Treatments
Mean expression
Inflorescence
Broader
Narrower
Flower
Narrower
Carpel
again
1) Estimation of
how strongly a gene is expressed
in different organs or tissues.
Chip Means for Tissues
Number of chips used for mean
OR:
Expression of chosen gene
Chip Means for Tissues
2) To identify genes expressed specifically in
chosen organs or tissues
and not at other chosen organs or tissues
>=95%
>=35% < 40%
highest signal: 100% (dark blue)
>=15% < 20%
absence of signal: 0 % (white).
>=5% < 10%
Genes (clustered)
Heat Map:
>=75% < 80%
White-blue (for absolute signal intensity values)
>=55%
< 60%control).
(red-black-green for treatment
versus
Higher expression
Some expression
Expression of chosen gene
Mean expression
1) Estimation of
how strongly a gene is expressed
throughout the life cycle
OR:
Genes (clustered)
2) identify genes expressed
specifically at chosen growth stages
and not at other chosen growth stages
Chip means for stage
Chip means for stage
OR:
Chip means for Treatments
1) Estimation of
how strongly a gene is expressed
in response to stimuli
Ratio
on Treatment chip + Control chip
Expression of chosen gene
Chip means for Treatments
Genes (clustered)
2) identify genes expressed
specifically at chosen treatments
and not at other chosen treatments
The expression profiles of up to 50 genes can be viewed as a
heat map
Visualise over:
Organs
Development
Treatments
Chip means for
Organs/Age/Treatment
Genes (clustered)
Lists of genes can be copied from a spreadsheet
Is the expression of a chosen gene affected by genetic modifications?
More than 100 genetic modifications used.
Genetic Modifications
Most are mutations.
With some RNAi, overexpression, etc.
Ratio
on Mutant chip
+ Control chip
Expression of chosen gene
1/--страниц
Пожаловаться на содержимое документа