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. 2011 Apr 20:12:109.
doi: 10.1186/1471-2105-12-109.

PheMaDB: a solution for storage, retrieval, and analysis of high throughput phenotype data

Wenling E Chang  1 , Keri Sarver, Brandon W Higgs, Timothy D Read, Nichole Me Nolan, Carol E Chapman, Kimberly A Bishop-Lilly, Shanmuga Sozhamannan
Affiliations

PheMaDB: a solution for storage, retrieval, and analysis of high throughput phenotype data

Wenling E Chang et al. BMC Bioinformatics. .

Abstract

Background: OmniLog™ phenotype microarrays (PMs) have the capability to measure and compare the growth responses of biological samples upon exposure to hundreds of growth conditions such as different metabolites and antibiotics over a time course of hours to days. In order to manage the large amount of data produced from the OmniLog™ instrument, PheMaDB (Phenotype Microarray DataBase), a web-based relational database, was designed. PheMaDB enables efficient storage, retrieval and rapid analysis of the OmniLog™ PM data.

Description: PheMaDB allows the user to quickly identify records of interest for data analysis by filtering with a hierarchical ordering of Project, Strain, Phenotype, Replicate, and Temperature. PheMaDB then provides various statistical analysis options to identify specific growth pattern characteristics of the experimental strains, such as: outlier analysis, negative controls analysis (signal/background calibration), bar plots, pearson's correlation matrix, growth curve profile search, k-means clustering, and a heat map plot. This web-based database management system allows for both easy data sharing among multiple users and robust tools to phenotype organisms of interest.

Conclusions: PheMaDB is an open source system standardized for OmniLog™ PM data. PheMaDB could facilitate the banking and sharing of phenotype data. The source code is available for download at http://phemadb.sourceforge.net.

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Figures

Figure 1
Figure 1
PheMaDB analytical module selection page. The analysis module menu page allows user to select specific analyses after identifying strains and phenotypes of interest.
Figure 2
Figure 2
Heat map of cell growth changes for AP50c mutant. The heat map provides an overall picture of the cell growth impact on the 1,920 phenotypes for AP50c mutant strain as compared to the wild type strain. The green shaded areas (PM01-PM08) indicate better cell growth of mutant strain whereas the black and darkly shaded areas (PM09-PM20) indicate relatively similar cell growth of the mutant strain as compared to the wild type strain. The PM1 through PM20 data are presented as blocks of 20 columns. The rows represent the 96 wells in each of the PM plates (A01 through H12). The bar at the bottom provides visualization of the fold change between the mutant and the wild type parent strains.
Figure 3
Figure 3
Bar plots for 8-Hydroxyquinoline. The bar plots indicate a decrease in cell growth for the AP50c mutant as compared to the wild type AP50c strain over a course of 72 hours. The top light blue bar plots represent 8-Hydroxyquinoline growth profiles located in PM20/G11 (left) and PM20/G12 (right) for the mutant strain. The bottom dark blue bar plots represent 8-Hydroxyquinoline growth profiles located in PM20/G11 (left) and PM20/G12 (right) for the parent strain.
See this image and copyright information in PMC

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