Download Pathway analysis

Pathway analysis
Daniel Hurley
Pathway analysis: summary
A popular buzzword…
but what does it mean?
How do you do it?
How do you interpret the
results?
First
What we mean by ‘pathway analysis’
• A ‘pathway’ implies causation, but don’t be fooled!
What we mean by ‘pathway analysis’
• A ‘pathway’ implies causation, but don’t be fooled!
• Most ‘pathway analysis’ actually identifies groups of
functionally similar transcripts.
• Louis’ example:
(http://gather.genome.duke.edu/)
What we mean by ‘pathway analysis’
• A useful paper….
But the conclusion is: lots of tools,
some quite different approaches!
What we mean by ‘pathway analysis’
• Pathway analysis tools like GATHER, DAVID, and
GeneSetDB typically rely on enrichment analyses to tell
us things.
• This set of techniques asks the question ‘of this set of
genes, how many share any particular function, and is
that more than we would expect by chance?’
• Example: the top 200 most differentially-expressed
genes by some ranking (e.g. adjusted p-value)
• Determination of ‘by chance’ is usually done using a
permutation (= Monte Carlo) approach
• Other ‘pathway analyses’ involve signatures of groups
of transcripts (e.g. using Principal Component Analysis)
What we mean by ‘pathway analysis’
But what do we mean by a ‘function’?
Lots of things:
Protein function
Hypothetical
protein function
Chromosomal
location
Metabolic
pathway
association
Disease
association
Daunting
The key
point
What we mean by ‘pathway analysis’
• Pathway analysis can
identify common features
present in a group of
transcripts
• What the output means
depends on the specific
biology under study
• No such thing really as a
‘general’ pathway analysis
• A good place to start is by
finding papers relevant to
the specific biology
What can you do with it?
Some answers:
Get a general picture
of the active functions
in a condition (vs.
control)
Identify conditions
with similar
functions
Investigate the
functions
associated with a
particular gene
Investigate whether
a particular function
is active in a
condition
Differentiate
conditions by their
active functions
Next
Pathway analysis: how you do it
• Begin with a list of transcripts of interest
Pathway analysis: how you do it
• Choose a web-based tool: GATHER, DAVID and
GeneSetDB are good ones to start
But Pathguide.org has 325
pathway links at last count
Pathway analysis: how you do it
• Enter the list of transcripts: with most tools, you will
either paste in gene names or identifiers, or upload a
file
Finally
Pathway analysis: interpreting results
• Basic tools will produce ranked lists of the most
‘enriched’ categories:
GATHER
Pathway analysis: interpreting results
• More sophisticated ones will produce ‘network’
diagrams
DAVID
Ingenuity Pathways
But the interpretation of these
is
Analysis
rather subjective
Summary
• Pathway analysis should probably be called information
enrichment analysis – a more accurate term
• Used prudently, it is a useful tool for exploring the
functional landscape of an experiment
• To make it meaningful, you need to interpret the results
in the context of the specific biology under study
• There are a lot of web-based tools; start with one which
is current and produces a result you value
• To start, you need a set of (transcripts) of interest
• To present the results, you can use a simple table, or a
more complex ‘network’ diagram
• Risk: false-positives are very difficult to identify, and
with enough data you can link any molecular species to
any other species
FIN
Any questions?