Transcript CWGIntroNew - Cell Wall Genomics

A tutorial on the Cell Wall
Genomics website
Bryan Penning
*Supported
bythe
theNSF
NSF
Supported by
Plant
Genome
Research
Plant Genome Researchand
REU
and
REUPrograms
Programs
Overview
• We will give a guided tutorial of the site and
how to access its information
– Guided tutorial – basic features of our site
– Guided tutorial – Fourier Transform Infrared (FTIR) data
– Guided tutorial – using the gene family trees at our site
• After this tutorial
– You will have an understanding of why this was undertaken
– You will be able to use the information available on our site
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Plant Genome Research
and REU Programs
Site Tutorial: Main Page
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and REU Programs
Between the blue bars are descriptions
and links to three cell wall sites. Top:
Oligogo at U. Wisconsin for tested
primers to the SALK lines. Middle:
CWG at Purdue for FTIR data, this
site. Bottom: UniformMu at U. Florida
for information on maize mutator
mutants in a W22 background
The main page provides links to
tutorials
The main parts of our site can be
accessed using the links in the upper
left hand corner of our site
A drop-down menu with links to our
group is located at the bottom of the
website
Site Tutorial: Introduction and Cell Wall
• The introduction page gives
background information on cell
walls and highlights some
methods used to study them
• The cell wall page gives a brief
overview of plant cell walls and
their architecture including the
major differences between
Type I cell walls found in
Arabidopsis thaliana and Type
II cell walls found in maize and
rice
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Site Tutorial: CWG mutants
• The Literature page lists
known mutants classified into
one of six classes (Class 1
shown)
• Clicking on 1.1 opens a page
of all known mutants for
Class 1.1 (MUR1 is shown)
• Each mutant has photos and
hypertext links to papers
relevant to the mutant where
available
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Site Tutorial: CWG Families
• The largest concentration
of information at our site
is contained in the CWG
families section
• Genes are classified into
six families plus an
unknowns section
• Clickable links open a page
showing all of the known
genes for that family in
table and dendrogram
(tree) form
• Clicking on 1.1 takes you to
the next page…
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and REU Programs
Site Tutorial: CWG Families
• Family 1.1 opens a new page
with tree diagrams for
Arabidopsis, rice, maize, and
a combined dendrogram
(direct links to their spot on
the page are at the top)
• Each tree image can be
clicked to open a FLASH
page
• Below each image is a link to
open the protein sequences
of the family members (You
can right click and choose
“save as” to download the
sequence information)
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and REU Programs
Site Tutorial: CWG Families
• Below the Arabidopsis tree is
a brief family description
and a table
• The table lists each gene
member and if available:
common name, SALK lines,
and a number of columns to
describe the FTIR spectra
type (information on FTIR
data can be found later in
the tutorial)
• The gene names are a
hypertext link leading to
Oligogo (see next page)
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Site Tutorial: CWG Families
• Clicking on a gene name in the table takes you to an outside link the Wisconsin T-DNA project (Oligogo) by O’Malley and
Patterson
• Gene At3g62830 is shown above where primers for SALK
insertions of that gene are listed and can be ordered
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Site Tutorial: FTIR Data
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On the families table are links
to excel files of wild type and
mutant spectral data (see our
FTIR tutorial for more
information
http://cellwall.genomics.purdue.edu/)
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Listed are the number of
principal components that give
greatest separation and the %
of individuals correctly
classified
A yes/no/maybe spectrotype
(yes >80%, 80% ≤ maybe ≥
70%, no < 70%) is given with a
link to interpreted data if
there is a mutant spectrotype
Site Tutorial: FTIR Data Page
• Information contained in
the PDF Files for FTIR
(likely spectrotype)
– Name and our data
interpretation
– Top left: Avg. spectra of
mutant and Wt (Col)
– Top right: Digital
subtraction of mutant
from Wt
– Bottom left: PCA cluster
plot showing separation
– Bottom Right: PC
Loading(s) contributing
most to separation
– See FTIR tutorial for
more information
http://cellwall.genomics.pur
due.edu/
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Plant Genome Research
and REU Programs
Site Tutorial: NIR Data
• Maize mutants showing
a NIR mutant
phenotype
– You can download the
wildtype spectra
from the W22
Spectra column
– You can download the
mutant spectra from
the Mutant Spectra
column
– You can see our
annotation in the
Spectrotype column
(next slide)
– See Techniques VIII
for details on NIR:
http://cellwall.genomi
cs.purdue.edu/techni
ques/8.html
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Plant Genome Research
and REU Programs
Site Tutorial: NIR Data Page
• Information
contained in the PDF
Files for FTIR
– Family: Name as
listed in the Maize
family data table
– Interpretation: Our
evaluation of the
data for important
peaks
– PLS loading:
Differences in
spectral values
between mutant and
wildtype
– PLS score plot:
shows separation of
particular reads for
mutant and wildtype
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Site Tutorial: CWG Families
• Clicking the Arabidopsis tree
opens a FLASH file family
tree as a radial dendrogram
with colored ovals denoting
tree clades of similar
sequence (1.1 shown)
• See how these trees are
made with our Tree Tutorial:
http://cellwall.genomics.purdue.
edu/
• Each oval can be clicked to
open a close up view of the
individual clade, such as
AUD/SUD (next page)…
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Site Tutorial: CWG Families
• In this view the AUD/SUD
clade of 1.1 is shown as a
radial dendrogram
• Clicking any gene name will
bring up a drop down menu
with links to information
outside of our site
• For Arabidopsis, we link to
TIGR, MIPs, TAIR, and SALK
• Clicking on any of these links
will open a gene information
page in a new window from
that source
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Site Tutorial: CWG Families
• Clicking on the TIGR button
opens a gene information
page from The Institute for
Genomic Research
• From this page you can
download the Genomic,
cDNA, or protein sequence
for this gene and find out
some basic information as to
its classification and
attributes
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Site Tutorial: CWG Families
• Clicking on the MIPs button
opens a page from the
Munich Information Center
for Protein sequences
• This site will give you any
known information about the
protein
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and REU Programs
Site Tutorial: CWG Families
• Clicking on the TAIR button
opens a page from The
Arabidopsis Information
Resource
• TAIR includes a host of links
and useful information on a
number of topics such as
annotations, bibliographies,
map positions, gene model
information, gene ontogeny,
and general information
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Site Tutorial: CWG Families
• Clicking on the SALK button
opens a page from SIGnAL
(the SALK Institute Genomic
Analysis Laboratory)
• This page shows all of the
SALK T-DNA insertions and
their location in the gene (a
vertical line runs down the
center of the gene and
through the SALK boxes)
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Site Tutorial: CWG Families
• As with the Arabidopsis
tree, you can click on the
Rice tree to bring up an
interactive FLASH file of a
radial dendrogram family
tree (1.1 shown)
• Clicking on the individual
clades of the radial
dendrogram brings up a
closer view such as AUDSUD-like…
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Site Tutorial: CWG Families
• Clicking on the AUD-SUD
clade brings up a close-up
view of that part of the tree
as a radial dendrogram
• There are clickable links for
each gene member
• The links for TIGR and MIPs
contain information just as
was shown for Arabidopsis
• The Orygenes and Gramene
buttons are new…
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Site Tutorial: CWG Families
• OryGenes is a site sponsored
by Cirad and is similar to
SALK for Arabidopsis
• For each gene, any available
insertion lines are shown with
their location in the gene
• OryGenes uses the same
genome browser (GBrowse)
that many sites, including
SALK make use of to display
information
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Site Tutorial: CWG Families
• The Gramene button links to
Gramene.org at the location
of that particular rice gene
• Gramene contains a wealth of
cereal synteny data including
gene model, sequence,
marker, and EST alignments
for many cereals such as
rice, maize, wheat, barley,
and oat
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Site Tutorial: CWG Families
• As with the Arabidopsis
tree, you can click on the
Maize tree to bring up an
interactive FLASH file of
a radial dendrogram of
the gene family members
• Clicking on the individual
clades brings up a closer
view such as AUD/SUDlike…
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Plant Genome Research
and REU Programs
Site Tutorial: CWG Families
• Clicking on the AUD/SUD
clade opens a close-up view
of the genes as a radial
dendrogram
• There are no clickable
links yet but we hope to
add some similar to the
rice links later
• The blue text indicates
gene fragments while
green text is full sequence
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Site Tutorial: CWG Families
• The combined dendrogram
link takes you to a square
dendrogram of Arabidopsis,
rice, and maize families (part
of 1.1 is shown)
• The red names are
Arabidopsis sequence, the
black names are rice, and
the green names are maize
• Regions alternate between
grey shaded and white
backgrounds to indicate
clades (such as AUD/SUD or
GME genes, etc)
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Site Tutorial: Techniques
• The techniques page has
links to descriptions of
many of the procedures we
use to gather our data and
that are useful to cell wall
biologists
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Site Tutorial: Web Links
• The web links page lists
sites with information
used in the construction
of our site and useful to
cell wall biologists
• After each link is a
short description of
what can be found at
the site
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Site Tutorial: Contacts
• The contacts page lists
contact information for a
number of our group
members to which you can
provide site feedback
• For more information on
trees, FTIR, or the
website you can also
contact Bryan Penning:
[email protected]
Supported by the NSF
Plant Genome Research
and REU Programs
Websites shown in this tutorial
• Cell Wall genomics: http://cellwall.genomics.purdue.edu/
• Oligogo: http://oligogo.botany.wisc.edu/
• UniformMu:
http://currant.hos.ufl.edu/mutail/Cell_Wall_Gene_Knockouts.html
• TIGR: http://www.tigr.org/
• MIPS: http://mips.gsf.de/
• TAIR: http://arabidopsis.org/
• SIGnAL: http://signal.salk.edu/
• OryGenes: http://orygenesdb.cines.fr/
• Gramene: http://www.gramene.org/
Supported by the NSF
Plant Genome Research
and REU Programs