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
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
Contact Information
Elizabeth S. [email protected] 1103, 550 Building410-614-2588
Giovanni [email protected] 1103 550 Building410-614-3426
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.
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.
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
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.
GeneX• Web based database, data mining, and data analysis tool• Supports * multiple users * multiple species * multiple microarray platforms
Common Denominator for data analysis
GeneX Components
• Curation Tool (imports data)• Database (OpenSource SQL)• XML Data Exchange Protocol• Query and analytic routines -- mining -- biostatistics in R
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
Regulation of extracellular matrix changes and fibrosis in inflammatory bowel disease.
Shukti ChakravartiFeng Wu
Department of MedicineJohns Hopkins University
TNBS-colon
Control
TNBS
TNBS-induced colitis modelTNBS dose time points (weeks)
Harvest
0 2 4 6 12
• RNA • Protein • Histology • Intestinal fibroblasts
Disease initiation
fibrosis
8
inflammation
acti
vity
time
inflammation
ECM/fibrosis
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
Normalization
FDR < 1/2
Empirical Bayes Ranking versus Statistical Significance
P-value < .05
Patterns of gene expression over time
Red: positive slope, low fdrGreen: negative slope, low fdr Orange and Brown: low p-value