IsoGeneGUI: a graphical user interface for analyzing dose ...
Transcript of IsoGeneGUI: a graphical user interface for analyzing dose ...
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: a graphical user interface foranalyzing dose-response studies in microarray
experiments
Research team:
Setia Pramana 1, Dan Lin 1, Ziv Shkedy 1, Tobias Verbeke 2,Philippe Haldermans 1,Willem Talloen 3.
1. IBioStat, Universiteit Hasselt, Belgium
2. OpenAnalytics, Belgium
3. Johnson & Johnson Pharmaceutical R&D, Belgium
useR! 2010 Conference, 21 July 2010, Gaithersburg, Maryland,USA
Background Test for Monotone Trend Software IsoGeneGUI Package
Overview
Background: Dose-response Studies
Test for Monotone Trend
The Software
Analysis using IsoGeneGUI PackageData exploration
Likelihood Ratio Test E2 analysis
Resampling-based analysis
Significance Analysis of Microarrays (SAM)
User defined graphical display
Background Test for Monotone Trend Software IsoGeneGUI Package
Dose-response studies
The fundamental objective ofdrug development is to find adose or a range of dose thatefficacious and safe.
Dose-response studyinvestigates the dependence ofthe response on doses.
Within a microarray setting theresponse of interest is geneexpression.
dose
gene
exp
ress
ion
0 0.01 0.04 0.16 0.63 2.5
67
89
10
Background Test for Monotone Trend Software IsoGeneGUI Package
Dose-response studies in Microarray Experiments
The aim is to identify a subset ofgenes with a monotone trend.
In general, increasing the dosewill result in a proportionalincrease in the response.
Estimation: Isotonic regressionwithPool-Adjacent-Violator-Algorithm(PAVA). 0.
51.
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03.
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doses
gene
exp
ress
ion
1 2 3 4
PAVA
*
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* *+
+ +
+
Background Test for Monotone Trend Software IsoGeneGUI Package
Testing for Monotonic Trend
Hypotheses: For gene i (i = 1, · · · , m) with K + 1 doses(j = 0, · · · , K )
H0 : µ(d0) = µ(d1) = · · · = µ(dK ) (No Dose Effect)
HUp1 : µ(d0) ≤ µ(d1) ≤ · · · ≤ µ(dK ) (Ordered alternative)
The likelihood ratio test (E201).
The t-type tests: Williams, Marcus, M and M ′
Lin et.al 2007
Background Test for Monotone Trend Software IsoGeneGUI Package
Testing for Monotonic Trend: Inference
Inference
Exact Distribution Resampling-based Inference
PermutationsLRT ( 2
01E )
Williams
Marcus
Significance Analysis
of Microarrays (SAM)
LRT ( 2
01E )
Williams
Marcus
M
Modified M
LRT ( SAM2
01E )
WilliamsSAM
MarcusSAM
MSAM
Modified M ( SAMM ' )
Both approaches will be discussed in the
next slides
Background Test for Monotone Trend Software IsoGeneGUI Package
Resampling-based Inference: Permutations
Observed test statistics E2:
E21 , E2
2 , . . . , E2m
Resampling-based Inference, the permutation matrix T :
T =
E211 E2
11 . . . E21B
E221 E2
22 . . . E22B
......
E2m1 E2
m2 . . . E2mB,
B is the number of permutations.
Raw p-values: Pi =#(b:E2
ib≥E2i )
B .
Background Test for Monotone Trend Software IsoGeneGUI Package
Significance Analysis of Microarrays (SAM, Tusher et al., 2001) for
microarrays under order restriction
A modified score is assigned to each gene.
For the t-type test statistics (i.e., Williams, Marcus, the M,and the M ′):
Original:
M ′=
µ⋆
K−µ⋆
0s′
Modified:
M ′SAM=
µ⋆
K−µ⋆
0s′+s0
s0 is the fudge factor added to protect against inflatedstatistic due to small standard errors.
Background Test for Monotone Trend Software IsoGeneGUI Package
Software
Software for dose-response in microarrays analysis:
R package: IsoGene, available in CRAN:http://cran.ii.uib.no/web/packages/IsoGene/
Pramana et.al 2010, The R Journal
R GUI package: IsoGeneGUI, available in theBioconductor project:http://bioconductor.org/packages/2.7/bioc/html/IsoGeneGUI.html
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: Main Window
Load Data
Data ExplorationAnalysis:
E201 exact distribution.
Resampling-basedInferenceMultiplicity adjustment(FWER and FDR)Significant Analysis ofMicroarrays (SAM)
Output & GraphicalDisplays
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: Data Format
The package can read data in the following formats:
R workspace (*.RData files)
Excel file (*.xls files)
text file (*.txt files)
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: Data Exploration
Exploratory Data Analysis
The Isotonic regression plots The summary statistic
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: The E201 Analysis
Antipsychotic study.6 dose levels4-5 samples at each doselevel.11,565 genes.The dataset is availableinside the package.
dose
gene
exp
ress
ion
0 0.01 0.04 0.16 0.63 2.5
67
89
10
The E201 test and BH-FDR (0.05)
are specified:
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: E201 Result
E201 with BH-FDR (0.05).
298 genes with significantmonotone trend
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: List of Significant Genes
List significantgenes.
The list be saved asan R object or/andan excel file
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: Volcano Plot
E201 vs. Fold change
The graph can be copiedinto clipboard and besaved into different imagetypes.
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: Resampling-based Inference
Required specification:number of permutations,test statistic and multiplicityadjustment.
The permutation result canbe saved and used later.
List of significant genesusing the selectedstatistic(s).
Graphical displays.
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: SAM (specification)
Required : Number ofpermutations and thefudge factor.
SAM regularized teststatistic, e.g.,:
M ′SAM =µ
⋆
K −µ⋆
0s′+s0
Delta (∆) is chosen withestimation of the FDR.
SAM permutation dialog box
Background Test for Monotone Trend Software IsoGeneGUI Package
IsoGeneGUI: SAM (Results)
Threshold/Delta: 0.68FDR: 0.0436Number of significant genes: 164Delta table:
Background Test for Monotone Trend Software IsoGeneGUI Package
User Defined Graphical Display
User can define their own figures:
Background Test for Monotone Trend Software IsoGeneGUI Package
Help
Html help with screen shots
Background Test for Monotone Trend Software IsoGeneGUI Package
More detail...
Book of Lin, D., Shkedy, Z., Yekutieli, D., Amaratunga, D., andBijnens., L., editors. Modeling Dose-response MicroarrayData in Early Drug Development Experiments Using R.Springer. To be published in 2010.IsoGene Project site:http://www.ibiostat.be/software/IsoGeneGUI/index.html
Thank you for your attention...