Transcript “My Experiment” and What I Want to Discover

“My Experiment” and What I Want to
Discover
• My experiment involved comparing the effect of long term ozone
exposure on gene expression in a wild type and a mutant genotype
(only one gene, Gene G, difference). Time points taken. What
effect does the mutated gene have on defense against ozone?
• The two genotypes showed a phenotypic difference under ozone,
e.g. the mutant genotype senesced sooner (got old) than the wild
type. Phenotype can be displayed as numbers on a time scale.
• I want to identify any pathways, or fragments thereof, and their
corresponding (hypothetical or proven) regulators, that behaved
differently between the two genotypes, starting with lists of genes.
• I want to be able to capture an image of that pathway fragment,
with the indication that ozone affected its function.
Reported Actions of Ozone
Senescence onset is a quantifiable phenotype, which is the consequence of
responses of processes and entities named in the boxes below,( transcription etc…)
.
Gene G
Modified from
Ludwikow A, Sadowski J.
J Integr Plant Biol. 2008 Oct;50(10):1256-67
Desiderata for Inference: A Fancy Output Doc
Anti-Aging for Plants.
• Access MapMan, PlantMetGen Map, to get information on enriched
metabolic and signaling pathways that are differentially affected by ozone
in the two genotypes. Images captured from the first two, with data
marked.
• Mine enriched GO terms/MapMan bins to search for possible regulators
that may have responded to ozone, e,g. possible components of signaling
pathways such as transcription factors/ protein kinases, or other
regulatory functions such as modifiers of chromatin structure, or small
RNAs.
• For example, putative Regulator X did not respond to ozone in the mutant
genotype. Regulator X and Pathway A were activated in the wild type
under ozone, and were unresponsive in the mutant genotype. Infer that
the Gene G that was mutated controls Regulator X which is essential for
defense against ozone, by protecting against early senescence (directly or
indirectly). Ability to draw, literally, draw, this inference.
• Yes, Greg, these are correlations! .
Drawing the Inference
The connection from Gene
G to the AND above
Regulator R is the inferred
causality link.
The change in onset of
senescence may be
exerted through the
hormones that respond
to ozone.
Perturbation
Phenotype
One Interpretation:
Pathway A operates
to control the time
of senescence onset.
Methods of Causal Inference*
• Granger Causality: Uses statistical correlation to
assess causality between two time courses
• Bayesian Networks: A network of conditional
probabilities used to build model; tested statistically
• Structured Equation Modeling: A network of
functional dependencies used to build model;
tested statistically
*Thanks to Björn for these.
Luck, or the Lack Thereof
• If we are very lucky, only one pathway, and one
putative regulator, will be identified as being
differently affected by ozone in the two genotypes.
• We could then draw a simple genotype to phenotype
inference.
• A much more likely result are data pointing to a
number of interlocking pathways. We could draw
that too!
Hormones and Ozone
When ozone is present, four plant
hormones respond, which
interact with each other.
1
4
3
2
Modified from
Ludwikow A, Sadowski J.
J Integr Plant Biol. 2008 Oct;50(10):125667
Another Version of Ozone Action
Interlocking pathways abound!
Wrzaczek* et al. BMC Plant Biology 2010, 10:95
iPlantOmicsVis
--Analysis & Visualization of Gene Expression, Proteomics and Metabolite Data
Effect of Environmental
Change on
Species/Genotypes,
Developmental Time Course
in Species/Genotypes
•Design info/file
•GEO#
•GOterm of interest
•RNAseq data*
•Metabolomics data*
•Proteomics data*
AffyGen
Analyser ®
G
U
User
•GenExpr2Ddata
•GenExprSum
•ContrastFiles
•EnrichedGO graphs
•GeneMANIA output
•G2P inferences
I
Statistically
Analyzed data*
* statistically analyzed data
MapMen
GO®
Analyser
ViVA
Enriched GO
terms/Bins/
Pathways
Cytoscape
BiNGO
Output
docs
Ondex**
Phenotypic
observations*
feed into ViVa/
output docs
** tools that provide
more information/
connections from the
literature
Plant
MetGenMAP
eFP **
GeneMANIA
**
Gene
List(s)