biostatistics bioinformatics core
DESCRIPTION
Biostatistics Bioinformatics Core. Personnel Elizabeth Garrett, PhD Biostatistician Giovanni Parmigiani, PhD Biostatistician Data analysis and System support staff Hardware DELL server; linux OS Linux and Windows workstations Software GeneX Database; R-based analysis tools - PowerPoint PPT PresentationTRANSCRIPT
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Biostatistics Bioinformatics Core
Personnel Elizabeth Garrett, PhD Biostatistician Giovanni Parmigiani, PhD Biostatistician Data analysis and System support staff
Hardware DELL server; linux OS Linux and Windows workstations
Software GeneX Database; R-based analysis tools Labs: Affy Suite, others TBA
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Contact Information
Elizabeth S. [email protected] 1103, 550 Building410-614-2588
Giovanni [email protected] 1103 550 Building410-614-3426
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Aims of the Biostatistics Core
Specific Aim 1:To provide biostatistical consultation and
support to projects in the program. Special emphasis will be to assist in
visualization, analysis, quantitative modeling and interpretation of results.
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Aims of the Biostatistics Core
Specific Aim 2:To help in identifying the appropriate data
structures; ensuring data quality and data confidentiality; and developing efficient data transferring and interfacing for data analysis and data visualization under different platforms.
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Two important stages where we get involved
• Planning Stage: – Experimental Design
• How many samples?• How many replicates?• Housekeeping genes?• Dye swapping?
– What’s the big deal? You could spend a lot of time and money and not able to answer your questions due to experimental errors, etc.
Before the study:How can I best address my hypothesis using minimal resources to get maximal information?
After the study:Now that I have this enormous amount of data, how do I summarizeit and answer my questions?
• Analysis Stage:– Visualization– Data Exploration– Analytic Tools and Models
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What we do• One-on-one consultations with investigators for
planning experiments• One-on-one consultations with investigators for
visualization, data exploration, and analysis.• Tutorials for helping investigators use some of the
software for exploration and visualization independently.
• Tutorials on basic statistical concepts, including experimental design in gene expression studies and basic analytic tools.
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GeneX• Web based database, data mining, and data analysis tool• Supports * multiple users * multiple species * multiple microarray platforms
Common Denominator for data analysis
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GeneX Components
• Curation Tool (imports data)• Database (OpenSource SQL)• XML Data Exchange Protocol• Query and analytic routines -- mining -- biostatistics in R
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Analytical Tools and Applications Included or Co-developed with GeneX
• Clustering• Visualization• Principle Component Analysis
and Multi-Dimensional Scaling• Significance testing with R• Integration with other databases
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Regulation of extracellular matrix changes and fibrosis in inflammatory bowel disease.
Shukti ChakravartiFeng Wu
Department of MedicineJohns Hopkins University
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TNBS-colon
Control
TNBS
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TNBS-induced colitis modelTNBS dose time points (weeks)
Harvest
0 2 4 6 12
• RNA • Protein • Histology • Intestinal fibroblasts
Disease initiation
fibrosis
8
inflammation
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acti
vity
time
inflammation
ECM/fibrosis
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Analysis Plan
• Expression estimates using dChip• Additional normalization for scanner effect• Two-level regression model• Identification of reliably estimable time
trends in gene expression• Grouping genes by patterns
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Normalization
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FDR < 1/2
Empirical Bayes Ranking versus Statistical Significance
P-value < .05
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Patterns of gene expression over time
Red: positive slope, low fdrGreen: negative slope, low fdr Orange and Brown: low p-value