Pathway Tools Overview and Omics tutorial script
March 16 2012 version
Alexander Shearer
To the instructor:
The Overview and Omics tutorial is done via live demonstration on the
desktop software and on the BioCyc site. You’ll want to have both up and available
before you begin. You will also want to have a sample gene expression data set for E.
coli ready on your computer (tutorial attendees should have the same file as well).
The file H2O2.txt is a 12-time-point time course of genome expression in coli
following exposure to hydrogen peroxide.
Rather than strictly script your exact words, each section lists information
you need to convey and actions to demonstrate.
One way to slow down a bit and enhance clarity is to clearly announce what
you are clicking on, and whether you are right or left clicking.
It’s also helpful to the tutorial participants if you mouse over any item you’re
discussing.
-- Pathway Tools Overview and Omics tutorial script starts here -All about the overviews
Desktop
One of the valuable features of Pathway Tools is the ability to approach vast
data sets through intuitive means – such as the pathway displays that show the
entire pathway and its internal regulation.
The biggest tools for this in Pathway Tools are the overviews and omics
viewers. They give you a comprehensive, all-in-one view of the biology of the
organism you’re looking at.
There are three overviews
The cellular overview, which looks at metabolism
The regulatory overview, which looks at transcriptional regulation
The genome overview, which looks at the whole genome
The cellular overview
The cellular overview is a snapshot of the organism’s metabolism
It shows all the metabolic reactions and compounds
Lines are reactions, nodes are compounds
Shown in pathways
Pathways are grouped by general types (for example “lipid biosynthesis”)
Cellular overview also shows all proteins that are localized to some place
other than the cytosol
Point out transporters as well
All objects clickable
If you right-click on an object, will get the choice of viewing that object, the
pathway its in, or other related data
Zooming
Can zoom in and out
Semantic zooming means that information appears and disappears
Highlighting and other display tools
Can show / hide links between transported compounds and those same
compounds inside the metabolic diagram
Can highlight reactions and pathways
Show highlight all by class
Show clear all highlighting
Show highlight by presence / absence in other organism
Can show other highlighting options, time permitting
The regulatory overview
Can display all the transcriptional regulatory relationships in the cell
Since Pathway Tools does not infer or predict regulatory data, a newly
generated PGDB won’t have a filled-in regulatory overview
Location in the overview already tells you something about the gene
Inner circle = regulating only
Middle circle = regulating and regulated
Outer circle = regulated only
Showing regulatory relationships
other
Can right click on any object in the overview
Chose to display direct and indirect regulators and regulates
Select a middle ring item and show direct regulates
Then show direct regulators for same
Genes in the outer ring batched by having exactly the same regulators as each
Can then display just the highlighted genes, effectively drawing out that
specific regulatory network
The genome overview
A schematic view of the organism’s genome
Unlike the genome browser, which is to scale and shows local context
If organism has multiple chromosomes or plasmids, all will be shown as
separate genomes on this one page
Genes shown in same color by transcription unit
Lines also show transcription units
Edges show direction of transcription
Top/bottom for edge shows whether genes are protein or RNA genes
Mouse over a gene for product, pathway, and gene distance information
Omics viewing
Omics viewing tools let you paint large-scale datasets onto these overviews
A quick way to comprehend enormous data sets
Cellular omics viewing
Same dialogue for all omics viewing
Select which overviews to use – can pick more than one at a time
For now, pick cellular overview
Upload file
Should have object names – say, genes – in first column
Then values in following columns
Walk through basic settings appropriate to your demo file
Display
Show information file – explain how it shows mismatch between your data
and the displayable items
Note that the majority of genes won’t display on overview
Details on viewing expression data
With default coloration, extremes set to biggest differences in data
Gene expression data is mapped onto reactions via enzymes
Biggest difference from set of isozymes is chosen for mapping onto reactions
Choosing colors
Default coloration shown
Can also set colors in many ways
Can set color cutoffs – for example, 0.9 and -0.9
Display data again
Multiple time points / conditions
Show setup for animation
Suggest using 6 time points – it shows a nice change over time, but doesn’t
take too long to load
If you use default color settings, normalized across all time points shown
So can be a good way to compare conditions
e.g. compare peroxide exposure to bleach exposure (no, we don’t have a data
set for this)
Genome omics viewing
Setup is the exact same as before, just pick genome overview
Show an example display
Show an example animation
Helpful in showing genes that matter in your data set which don’t map onto
other overviews
Can see whether predicted TUs express together or not
Regulatory omics viewing
Again, same setup
Show an example display
Show an example animation
Note how expression changes don’t match up perfectly with “co-regulated”
groups – points toward areas where more can be learned about your organism