Supported by the NSF Plant Genome Research and REU Programs

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A tutorial on the Cell Wall Genomics website
Bryan Penning
Supported by the NSF Plant Genome Research and
REU Programs
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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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Site Tutorial Main Page

• 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

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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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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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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 OMalley 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

• 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/)
• Listed are the number of principal components
  that give greatest separation and the of
  individuals correctly classified
• A yes/no/maybe spectrotype (yes gt80, 80
  maybe 70, no lt 70) is given with a link to
  interpreted data if there is a mutant spectrotype

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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.purdue.edu/

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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.genomics.purdue.edu/techniques/8.h
  tml

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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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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
  AUD-SUD-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/SUD-like

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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
  bpenning_at_purdue.edu

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Websites shown in this tutorial

• Cell Wall genomics http//cellwall.genomics.purdu
  e.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/