About Pheno-Pub

  We have developed a database system named "Pheno-Pub" to support a series of data handling and publication tasks, including statistical analyses, data review and website construction, for mouse phenotyping experiments. This system is composed of three applications. "Mou-Stat" provides semi-automatic statistical analyses for a batch of phenotypic data. "Genotype Viewer" and "Strain Viewer" provide two types of representations of genotype-driven and measurement parameter-driven views of phenotypic data; they show significant differences in genotype and summary views of differences in phenotypic measurement parameters among multiple strains, respectively.
  In the integrated workflow, tables and graphs of statistical results generated by Mou-Stat are uploaded to the Genotype Viewer to facilitate total website design. Descriptive statistics are also uploaded to Strain Viewer to generate graphical views of phenotypic comparisons among strains. The integrated workflow that processes experimental raw data to an organized website presenting phenotypic data is summarized in Figure 1.
  Mou-Stat was developed for high-throughput performance of routine phenotyping analyses based on implementation of statistical methods composed of R scripts. An integrated statistical workflow with multiple bunches (18 total analysis flows) is programmed to respond for different conditions for multiple criteria: scales of measurements (nominal, ordinal and rational), number of independent variables (one or two), number of groups (two or more than one), dependency of groups (repeated measurement or not), data distribution pattern (equal variance or not), and types of effects (detection of main effect and/or interaction) (See Figure 2). From a batch of phenotypic data, tables and graphs of statistical results on every test parameters are generated automatically at a time.

  Genotype Viewer is a webpage content management system for the representation of phenotypic differences based on statistical comparisons among mice of different genotypes. This application processes a batch of output files from Mou-Stat and additional image, movie and text files to arrange them programmatically in the resultant website. On the generated website, phenotypic data are summarized in a hierarchical structure with five levels which represent an overall summary, lower-level summaries, and detailed results by stage allow users to understand complex mutant phenotypes based on multiple results of measurement parameters (Refer to page of " About Genotype Viewer").

  Strain Viewer was designed to provide summaries of phenotypic differences among cohorts (e.g., mutants and inbred strains). This web application generates three types of figures dynamically: a bar graph for one measurement parameter, a scatter plot for two measurement parameters, and a list of the mean values for all of the measurement parameters (Refer to page of " About Strain Viewer"). In addition, multiple links to Genotype Viewer from the summary table provide quick access to comprehensive and detailed phenotypic data in a specific cohort.

  Japan Mouse Clinic (JMC) is a comprehensive mouse phenotyping platform open to the mouse genetics community and a member of International Mouse Phenotyping Consortium (IMPC). JMC has multiple pipelines for "On demand Clinic" (Fundamental pipeline and behavior-oriented pipeline) and for IMPC (Adult pipeline and Embryo pipeline).

  In this website, phenotypic information of various mice resources screened in JMC is shown using "Pheno-Pub" system. You can choose the viewer according to what you want to know. This system is freely downloadable from “Application download” page.


Fig. 1. Flow chart of tasks for the publication of data on the Internet using Pheno-Pub

about-pheno-pubn_01.png


Fig. 2. Programed statistical workflow implemented in Mou-Stat

about-pheno-pubn_02.png

                    *: An alarm message is displayed for unequal variance.
                    **: Subsequent multiple comparison tests can be executed at users' request.