PheMaDB: A Database for Analyzing Phenotype Data
Author Information
Author(s): Chang Wenling E, Sarver Keri, Higgs Brandon W, Read Timothy D, Nolan Nichole ME, Chapman Carol E, Bishop-Lilly Kimberly A, Sozhamannan Shanmuga
Primary Institution: The MITRE Corporation
Hypothesis
The extracellular material may alter the permeability and entry of compounds and nutrients and thus might alter the phenotype profiles as measured by OmniLog™ phenotype microarrays.
Conclusion
PheMaDB is an open source system standardized for OmniLog™ PM data that facilitates the banking and sharing of phenotype data.
Supporting Evidence
- PheMaDB allows users to filter data by Project, Strain, Phenotype, Replicate, and Temperature.
- The system provides various statistical analysis options including outlier analysis and k-means clustering.
- PheMaDB can produce publication-quality figures based on the analysis of phenotype data.
Takeaway
PheMaDB is a tool that helps scientists store and analyze data about how different organisms grow under various conditions.
Methodology
PheMaDB was developed using PHP for the GUI, R for analytical modules, MySQL for the database, and Perl for data parsing.
Limitations
The system has only been fully tested on Mac Operating Systems and may require further testing on Linux/Unix platforms.
Statistical Information
P-Value
9.97 × 10-6
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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