IMPC data portal documentation

Explore
The Gene page contain several subsections which will be described here.
  • Gene summary
  • Phenotype Associations
  • Phenotype Heatmap
  • Expression
  • Associated Images
  • Disease Models
  • Order Mouse and ES Cells

Gene Summary

The first section of the page shows summary information about the gene. The information displayed includes:
  • Name
  • Synonyms
  • MGI Id Links to the corresponding gene detail page at Mouse Genome Informatics
  • Status The latest IMPC production status for this gene. This aggregates the ES and mouse production statuses as well as phenotyping statuses of all ongoing projects for this gene in iMits and displays the status of the project that is closest to producing a mouse.
  • Links Links to different views of the gene in the Ensembl genome browser
    • Ensembl Gene Links to the browser centered on the gene
    • Ensembl Compara Links to a view of the cross-species resources and analyses, at both the sequence level and the gene level provided by Ensembl
  • Other Links
    • IMPC Gene Browser Interactive graphical gene browser. Clicking the link shows a genome browser displaying a graphical view of the gene's location and surrounding features. The browser is interactive and you can use your mouse to zoom and scroll.
    • ENU Links to the ENU mutant library at the Australian Phenomics Facility
  • Viability Shows lethality in homo-/hemi-/heterogyzosity background

Phenotype associations

This section shows the association of genes to Mammalian phenotype terms.

It contains 4 ways of data viewing:

(1) See all adult phenotypes
(2) See all embryo images, when available
(3) A quick glance of how phenotypes were discovered by icons
(4) Table view of significant phenotypes

(1) See all adult phenotypes:

Press the "All Adult Data" button.

You will be taken to a separate page for details of the statistical analysis. Significant P values appear to the right of the green dashed vertical line; insignificant values to the left. Hovering over any point shows some important experiment details. Clicking on any point shows a graph of the experiment data.

(2) See all embryo images:

Press the "3D Imaging" button.

You will be taken to a new page with an interactive graphical interface with which you could view the embryos




(3) A quick glance of how phenotypes were discovered by icons:

The icons on the right hand side show a visual summary of the same data. The colors indicate how significant phenotypes were discovered.

(4) Table view of significant phenotypes

This phenotype table lists the individual phenotypes associated to this gene through a specific allele. If both sexes are associated, then both are shown on the same row indicated by the male / female icons ().

The results shown in the phenotype table may be filtered using the dropdown filters. Select the check boxes to include entries pertaining to the selection. The displayed rows are the result of logically ORing within and logically ANDing between dropdowns.

Filter be top level MP term

Gene-phenotype association download

The results in the table may be downloaded for further processing. The resulting download respects all filters that have been applied to the data.

We offer 2 export options for the data in the table:

  • TSV, text file with tab separated variables
  • XLS, Microsoft Excel spread sheet

In the table displayed on our page entry lines are collapsed based on sex. That is, if for 2 lines all fields are identical except the gender, they will be shown together for a better user experience. In the export file however we export all lines separately, to allow easier further processing of the data. This holds for both XLS and TSV files.

Phenotype Heatmap

When there is data available, but not yet complete, from the IMPC resource, the Pre-QC panel will appear. The pre QC panel shows a heatmap of the results of preliminary analysis on data that has been collected by the IMPC production centers to date, but is not yet complete. In order to be marked Complete, 7 males and 7 females must complete all core screens required by the IMPC pipeline.

Please visit the comprehensive heatmap documentation for more information about the heatmap.

Please visit the IMPReSS website for more information about the IMPC pipeline.

NOTE: Use this analysis with caution as the analysis is likely to change when more data becomes available.

Below is an example of a typical IMPC heatmap.


Expression

This section displays IMPC lacZ expression data (A). In some cases where legacy lacZ expression data is available (B), they will be shown as well.


(1) IMPC lacZ Expression Data:

Eventually, all genes should have both embryo and young adult (weeks 9-16) expression data. They are organized in tabs.

  • Adult Expression tab

    An anatomogram displays all lacZ expressing tissues in blue. Mouseover will light up a tissue currently under the cursor. Click on a tissue in the list will take you to a page with expression images.

    Click on "Show expression table" on top right corner will display expression data in a table. Click again to hide it.

    The Expression Data Overview tab is a summary of the number of animals assessed for a given tissue, the number of times positive staining for LacZ was observed, and links to uploaded images. Images for tissues not exhibiting LacZ staining are not typically uploaded.

  • Adult Expression Image tab

    Click on this tab to see all images expressed in the tissues shown in the "Adult Expression" tab.


  • Embryo Expression tab

    Click to show expression data in table by tissues.


  • Embryo Expression Image tab
  • Some IMPC centers are assessing the expression of a LacZ reporter element contained as part of the allele constructs. Histology images stained to show LacZ images are presented along with metadata describing the tissue assessed. The number in parentheses indicates how many images are available for a given image.

(2) Legacy lacZ Expression Data:

The data are organized by anatomy terms from the Mouse adult gross anatomy ontology.

Phenotype Associated Images

A number of assays generate image data and are used by the phenotyping centers to score the presence or absence of an abnormal phenotype. Uploaded phenotype images are presented here organised by the procedure generating the image. In addition to the IMPC images, some genes have legacy ones.

The screenshot below shows the number of images grouped by procedures. Click to reveal the content.

Disease Models

Model organisms represent a valuable resource for the characterization as well as identification of disease-gene associations, especially where the molecular basis is unknown and there is no clue to the candidate gene’s function, pathway involvement or expression pattern.

Shown here are human diseases found by PhenoDigm analysis (PHENOtype comparisons for DIsease and Gene Models) which uses a semantic approach to map between clinical features observed in humans and mouse phenotype (either from MGI or IMPC phenotype evidences) annotations.

The human disease model associations are based on gene orthology or phenotypic similarity that you can browse by clicking on the respective tabs.

In the table, each row is a human disease to mouse phenotype association. To see what mouse genes (alleles) are annotated to these mapped mouse phenotypes, clicked on the "plus" icon.

Order Mouse and ES Cells

The alleles and ES cells section describes the mutations available from the IKMC resource. Each row corresponds to an allele of this gene. A diagram is included depicting the mutation the allele carries.

The links in the Order/Contact column will take you to the purchase place of the ES cell or mouse when available.

The genbank file link points to a genbank file describing the genomic sequence of the allele.


Our phenotype page consists of three main parts: the phenotype information/details, the gene associations summary and the table of gene variants associated with the current phenotype.

Phenotype Summary

The synonyms and definitions we provide come from the mouse phenotype ontology (MP), which is administered by Mouse Genome Informatics (MGI). Use the provided MGI link to go to the MGI MP browser.

The procedures come from IMPC pipelines and from legacy data pipelines such as EUMODIC and GMC.

Phenotype Association Stats

IMPC mouse strains are subjected to a wide range of phenotype assays, allowing for estimates on the percentage of genes that, when knocked out, contribute to a phenotype. As multiple parameters may map to the same phenotype, percentages are calculated across all parameters that map to a phenotype.

The percentage of genes associated to the current phenotype in one sex only (for example, females) is the number of genes associated to phenotype X in females divided by the total number of genes tested in females for parameters potentially leading to phenotype X associations. Thus, the percent values we show for females and males may not add up to 1, nor do the percentages for males/females have to be smaller than the combined percentage.

We consider "tested" for a phenotype a gene for which at least one parameter potentially leading to this phenotype association has data and has been statistically analyzed by our pipeline.

Currently the data used for this panel is restricted to IMPC data on B6N strains. Mutant strains with the phenotype associations appear in the gene-phenoytype table found further down the phenotype page.

Overview Graphs

As the data is extremely varied, for instance, in what controls are selected, what is represented (e.g. individual animals vs strains), and the nature of the values (e.g. means, count, etc.), each is described separately below.

Chart Filters and Selectors

Multiple parameters can indicate the same phenotype. When this is the case, a drop-down list will appear on top of the list allowing you to select the desired parameter.

The filters under the chart allow you to filter the plotted data based on sex and phenotyping center.



Unidimensional Data

Unidimensional data is plotted as stacked histograms. We take the mean for each line and plot these values as a histogram. Mutant lines that have been associated to the phenotype are highlighted, including those lines where the phenotype was only observed in one gender or zygotic state. Some lines may be associated to a phenotype but may not appear to be an outlier. This usually results from controls having relatively low or high values in the time period the mutant lines were tested.

[Tip] The bars are clickable and will take you to a multi-chart page to analyze the data more closely.



Categorical Data

Categorical overview charts represent the percentage of strains in each category. These graphs only display for categorical parameters at the line level (as opposed to animal level), such as fertility or viability parameters. The animal-level parameters can only be analyzed in the individual charts linked from the associations table.

Gene-Phenotype Associations

All gene variants associated with the current phenotype are shown in a table. The table contains several fields of interest, such as the gene name and the corresponding allele, zygosity, sex, data source, parameter, a link to the chart when one is available, as well as the procedure used, and directly associated phenotype. The directly associated phenotype is particularly useful for higher level phenotype terms. See Direct vs. inferred associations for more information.

Row Collapsing

For better readability, when rows are identical in all fields except for sex, they are collapsed into a single row. Such rows are identified by a both-sexes icon (). Regardless of row collapsing, the total number of results shown at the top of the table includes all males and all females.



Direct vs. inferred associations

Some associations are direct calls from our statistical pipeline, whereas some are transitively associated, infered from the direct lower level associations. The value in the 'Phenotype' column will help you disambiguate at which level the gene-phenotype association was made.

Pre-QC vs. Post-QC Calls

Preliminary statistical analysis is performed at the DCC as soon as enough data is gathered, prior to rigorous quality control checking. This analysis produces results, but due to the preliminary state of the QC checks, the results are considered not definitive. Once the data has passed the QC checks at the DCC, a final definitive statistical test is performed and the MP association is made.

Post QC calls are presented in the associations table and have blue chart links.

Pre-QC calls are presented in the associations table and have orange chart links in that table and in the heatmap below the table.

Table Filtering

The filters over the gene variants associations table offer flexible filtering possibilities. Multiple checkboxes can be selected from any filter dropdown list and the table will automatically reload with each new selected option. These changes will be mirrored by the total number of results over the table as well as by the table export.

Multiple filters from the same dropdown list are joined by a logical OR. Filters between different lists are joined by a logical AND.

Downloading Results

The results in the table may be downloaded for further processing. The resulting download respects all filters that have been applied to the data.

We offer two export options for the data in the table: text file with tab separated variables (TSV) and Microsoft Excel spread sheet (XLS)

Please note: while collapsed rows are shown on the page, download file rows are not collapsed; the download file contains a single row for every mouse.

More information about the way IMPC uses disease data.

Explore Disease Data

The ultimate goal of studying model organisms is to translate what is learned into useful knowledge about normal human biology and disease.

The IMPC disease details page contains known gene associations (via orthology to human disease genes) and known mouse models from the literature (from MGI) for the disease as well as predicted gene candidates and mouse models based on the phenotypic similarity of the disease clinical symptoms and the mouse phenotype annotations. The phenotypic similarity is calculated using the PhenoDigm algorithm (Phenotype comparisons for DIsease Genes and Models) developed by the Monarch Initiative which will allow integration of data from model organisms to identify data-supported gene candidates for human genetic diseases (Link to Methods). Mouse Genotype-Phenotype and Human disease resources are described below.

Disease details pages

Results are broken down in 2 parts, depending on the association methodology (by gene orthology or by phenotypic similarity).

Clicking the row for a disease/gene will expand the row to show the details of the phenotype terms involved in the association between the disease and the mouse model. The orange number next to the genotype is the PhenoDigm score (see below) which is a percentage-based score . These are ranked from highest to lowest in two groups. The first group will show the manually curated mouse models from MGI. The second group will list the purely phenodigm predicted associations.

1: By Gene Ortholgy
Human genes/regions causing human disease were extracted from human disease resources described above. Matching mouse orthologues were identified from HomoloGene and associated mouse models were retrieved from IMPC and MGI resources. Phenotypes corresponding to mouse models were then compared to human phenotypes gene matched human disease using PhenoDIgm. Depending on the similarity between the phenotypes, a PhenoDigm score is calculated based on the number and specificity of the matches between the human and mouse phenotypes where 100% represents a perfect match and 0% no match.

2: By Phenotypic Similarity
We compared Mouse and Human Phenotypes using Phenodigm to provide evidence about gene-disease associations. Mouse phenotypes were extracted from mouse models from the IMPC and MGI repositories. Mouse phenotypes were then compared with human disease/phenotypes extracted from human disease resources (OMIM, ORPHANET, DECIPHER) using PhenoDigm as above. In this interface, we only display high-scoring (> 60%) matches that show a reasonable phenotypic similarity between the two species.

Human disease resources

Source Description
OMIM (Online Mendelian Inheritance in Man) An Online Catalog of Human Genes and Genetic Disorders
Orphanet The portal for rare diseases and orphan drugs
DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resource) Interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants

Mouse Genotype-Phenotype resources

Source Description
IMPC (International Mouse Phenotyping Consortium) Functional catalogue of mouse mammalian genome
MGI (Mouse Genome Informatics) International database resource for the laboratory mouse

The anatomy page represents the gene expression status generated using lacZ profiling for a particular organ/tissue.

More information about the way IMPC uses graphs.


Where is the data coming from?

Data for the charts are obtained from the IMPC phenotyping centers and from the Europhenome legacy project. The table of genotype to phenotype associations on the gene and phenotype pages includes links to charts of the data and more information about the processing used to determine statistical significance.

The P values and other model fitting estimates are calculated using the IMPC statistical methods.

Interacting with Graphs

Charts are interactive so that you can adjust the view to your liking. Click on a legend to remove a set of data from the graph. This is especially useful if you wish to remove "noise" from a chart and focus on the control or experimental data.

After clicking on the control legend, the male homozygote data has disappeared:

chart with no control here

Hovering over a data point or error bars displays extra information about the data point:

chart with a hovering over mouse label here

If appropriate, the chart will allow you to zoom in on a data set by clicking and dragging to create a square/zoomable area:

Scatter chart with no zoom shown here

Once zoomed, a "Reset zoom" button appears at the right of the chart to enable the chart to be reset to original position:

Zoomed in chart here

Parts of the chart header are also interactive. Clicking on the pipeline and procedure links will take you to the IMPReSS page describing them.

Chart header



Exporting Chart Data

An export button is always visible on the right hand side of the charts where the chart picture can be exported in png, jpeg, pdf or svg format which will be downloaded to your computer: export button in chart here

The data used to generate the charts can be downloaded in TSV or XLS formats from the buttons on the top of the page (export button in chart here). This will export data for all charts shown on the page. Data for males and females from the same experiment will be shown in the same table while for different zygosities, organizations or strains there will be separate tables exported in the same file. Following we present a list of exported values accompanied by a short description when needed.

Column Description
pipelineName Pipeline through which the phenotyping was done, e.g. EUMODIC pipelines
pipelineStableId Pipeline id
procedureStableId Procedure id
procedureName Procedure name
parameterStableId Parameter id
parameterName Parameter name
strain Mouse strain used
geneSymbol Gene symbol
geneAccession Gene MGI accession id
organisation Organization name
colonyId Colony id
dateOfExperiment Date of experiment
externalSampleId Animal id
zygosity Zygosity
sex Sex
group This field has only 2 values: control or experiment
category Column is exported only for categorical data. It contains the label of the category assigned.
meta data Shows any meta data in respect of equipment used which can be used to seperate the data sets used for statistical analysis
dataPoint Coulmn is exported for unidimensional or time series data. It contains the value resulted from the measurment decribed by the current procedure.
discretePoint Column exported for time series data. It contains the relative timepoints at which the measurments were made.

A restful web service (with Documentation) is also available for retrieving information pertaining to experiments via a web browser or a programming language of your choice.

Types of Charts and Equations

The following types of chart exist in the IMPC portal from the IMPC:

  1. Categorical Bar Graphs
  2. Unidimensional Scatter and Box Plot Graphs
  3. Time Series Graphs
  4. Pie Graphs graphing viability
  5. ABR graphs showing auditory brain stem response


Categorical Bar Graphs

Categorical charts contain data where an observation can be categorised into one of two or more groups e.g. Abnormal Eye or Normal Eye. Charts are presented as bar charts with a table underneath. If IMPC data is available this will be displayed (see statistics help for more information).

Unidimensional Scatter and Box Plot Graphs



Where an observation can be measured on a continuous basis (e.g. red blood cell counts or tail length), we display them in a mixed box and scatter plot. The first columns contain box plots for Wild Type (control), Homozygote then Heterozygote mutants for female, then the columns representing males. The second set of columns contains scatter plots for the same sets of data. Hover over the box in the chart to see the basic statistics for that set of data.

When the data for a parameter is collected at various points in time, a scatter plot shows each data value on the y-axis and the date/time the data was collected on the x-axis.

Below the chart is a table showing the output of the statistical test used to determine if this data is statistically significant:


In the top left of the table is the global P value used to determine if this is a statistically significant result.
The Classification column displays the effect of sexual dimorphism on this association (sexual dimorphism is the phenomenon when the genotype affects the sexes differently). The possible results are:

No significant change
The effect is not statistically significant
Cannot differentiate genders
For the measured parameter, there is a significant effect, but there is not enough statistical power to determine sexual dimorphism
Both genders equally
For the measured parameter, both sexes are affected equally
Female only
For the measured parameter, only the females are affected
Male only
For the measured parameter, only the males are affected
Different effect size, females greater
For the measured parameter, there is an effect on males but the size of the effect on females is greater.
Different effect size, males greater
For the measured parameter, there is an effect on females but the size of the effect on males is greater.
Female and male different directions
For the measured parameter, the effect on one sex is increased while the other sex is decreased.
If phenotype is significant it is for the one genotype tested
For the measured parameter, there was no data for one of the sexes, so sexual dimorphism cannot be determined.

The more statistics link at the bottom of the table displays additional output related to the statistical method.

Time Series Graphs

Where an observation can be measured as a time series (e.g. mean blood glucose concentration), we display the data in a line chart and scatter plot. The line chart will contain lines for wild-type and mutant data for female and for males. The data points displayed are the mean of all data collected at that timepoint and the whiskers indicate standard deviation. Hover over the points to see basic statistics about the data.

Pie Graphs

Pie graphs are used to display the results of the primary viability screen. The screen is used to assess the postnatal viability, sub-viability, and lethality of homozygous mice during cohort production.

ABR Charts

Auditory Brain Stem Responce data is plotted in the context of the whole serie of ABR measurements, as opposed to plotting each parameter separately. We plot data from the following parameters: click, 6kHz, 12kHz, 18kHz, 24kHz, 30kHz, where the click is separated from the rest of the data. For each parameter we plot the mean of it's respective measurements. If one parameter does not have any points it means no data is available.

Landing Page

The IMPC is capturing a broad, complex suite of phenotype data across biological systems for both embryonic and adult knockout mice. To address specific communities, IMPC informatics is developing specialised landing pages that highlight relevant data. The first of these is for embryonic phenotyping with other pages planned for the vision, auditory, cardiovascular, metabolism and bone/cartilage research communities.

Embryo Phenotyping landing page

The embryo phenotype landing page is available here.

This page summarises the different types of embryonic phenotype data being collected by the IMPC community and is organised into modules.

Viability module

The first module contains a graphical summary of the viability of knockout mouse strains characterized by IMPC centres. Next to it is a numerical summary organised by gene and a download button to allow users to obtain spread sheets of the data. All data is automatically updated with each data release.

Goals and Procedures

The second module contains information about the goals of the IMPC for embryonic phenotyping and the procedures used. Links to related grants funded to perform in depth phenotyping of IMPC embryonic lethal strains are included.

Two-dimensional imaging

The next module contains a summary of the 2-D imaging performed on IMPC embryonic lethal and subviable strains. Links are provided to thumbnail galleries that are updated with each data release.

Three-dimensional imaging

Three-dimensional imaging- This module provides links to 3-D embryo imaging data using micro-CT and OPT technologies. Refer to the previous section for more about the interactive embryo viewer.

Vignettes

This module captures vignette summaries of embryonic lethal and subviable mouse strains deemed interesting by IMPC developmental biologists. The left and right arrow heads scroll to individual vignettes. Clicking on the "Full Analysis" button at the end of the summary will take you to a more detailed vignette module (example next page)...

Detailed vignette

This view obtained by clicking on the "Full Analysis"" button from the vignette summaries contains a text description curated by IMPC biologists, links to relevant data contained in the IMPC database, and annotated images that provide additional information. Users can scroll up and down this page to see other detailed vignettes. To return to the Embryo Landing page, users will use the browser's back button.

Embryo Phenotyping Pipeline

The last module contains a graphical representation of the embryo phenotyping pipeline. Clicking on the image will take users to the IMPReSS resource that contains all the standardized protocols used the by the IMPC including those for embryo phenotyping.

  • Data release overview
  • Training
  • Communication material
  • Interact with graphs


  • Data Release Overview Documentation

    Data Release Overview Documentation

    The data release page summarizes all the significant Mammalian Phenotype (MP) statistical calls for one phenotyping center and pipeline. This information can be visualized in a graph and is also available in a table below the graph. To get to the visualisation:

    1. 1. Click the release link from the footer of any page to get to the release page.

      Link to release page image

    2. 2. Scroll down the release page to the Phenotype Associations Overview section and click on the Browse link for the phenotyping center and pipeline you want to browse. Link to phenome browser image

    Phenome Graph

    The graph section of the page shows a summary of all significant genotype to phenotype associations for mutant lines phenotyped by a specific mouse genetics clinic and pipeline. The information is organized by top-level phenotype categories:

    • immune system
    • hematopoietic system
    • homeostasis/metabolism
    • growth/size/body
    • skeleton
    • hearing/vestibular/ear
    • adipose tissue
    • cardiovascular system
    • vision/eye
    • behavior/neurological
    • pigmentation
    The x-axis indicates each MP term from each top-level category. The y-axis is a log transformation of the original P value for better interpretation. Each data point corresponds to a significant hit for a specific mutant line.

    Graph details

    A click on each data point will open a pop-up window that will display the details of the underlying data in a graph.

    Phenotype table

    The detailed phenotype section of the phenome page shows all the association of genes to Mammalian phenotype terms for a specific phenotyping center. The table mirrors the graph view and displays the following information in sortable columns:

    • Gene / Allele
    • Procedure
    • Parameter
    • Zygosity
    • Phenotype
    • P value
    • Graph




    More information about the way IMPC uses graphs.


    Where is the data coming from?

    Data for the charts are obtained from the IMPC phenotyping centers and from the Europhenome legacy project. The table of genotype to phenotype associations on the gene and phenotype pages includes links to charts of the data and more information about the processing used to determine statistical significance.

    The P values and other model fitting estimates are calculated using the IMPC statistical methods.

    Interacting with Graphs

    Charts are interactive so that you can adjust the view to your liking. Click on a legend to remove a set of data from the graph. This is especially useful if you wish to remove "noise" from a chart and focus on the control or experimental data.

    After clicking on the control legend, the male homozygote data has disappeared:

    chart with no control here

    Hovering over a data point or error bars displays extra information about the data point:

    chart with a hovering over mouse label here

    If appropriate, the chart will allow you to zoom in on a data set by clicking and dragging to create a square/zoomable area:

    Scatter chart with no zoom shown here

    Once zoomed, a "Reset zoom" button appears at the right of the chart to enable the chart to be reset to original position:

    Zoomed in chart here

    Parts of the chart header are also interactive. Clicking on the pipeline and procedure links will take you to the IMPReSS page describing them.

    Chart header



    Exporting Chart Data

    An export button is always visible on the right hand side of the charts where the chart picture can be exported in png, jpeg, pdf or svg format which will be downloaded to your computer: export button in chart here

    The data used to generate the charts can be downloaded in TSV or XLS formats from the buttons on the top of the page (export button in chart here). This will export data for all charts shown on the page. Data for males and females from the same experiment will be shown in the same table while for different zygosities, organizations or strains there will be separate tables exported in the same file. Following we present a list of exported values accompanied by a short description when needed.

    Column Description
    pipelineName Pipeline through which the phenotyping was done, e.g. EUMODIC pipelines
    pipelineStableId Pipeline id
    procedureStableId Procedure id
    procedureName Procedure name
    parameterStableId Parameter id
    parameterName Parameter name
    strain Mouse strain used
    geneSymbol Gene symbol
    geneAccession Gene MGI accession id
    organisation Organization name
    colonyId Colony id
    dateOfExperiment Date of experiment
    externalSampleId Animal id
    zygosity Zygosity
    sex Sex
    group This field has only 2 values: control or experiment
    category Column is exported only for categorical data. It contains the label of the category assigned.
    meta data Shows any meta data in respect of equipment used which can be used to seperate the data sets used for statistical analysis
    dataPoint Coulmn is exported for unidimensional or time series data. It contains the value resulted from the measurment decribed by the current procedure.
    discretePoint Column exported for time series data. It contains the relative timepoints at which the measurments were made.

    A restful web service (with Documentation) is also available for retrieving information pertaining to experiments via a web browser or a programming language of your choice.

    Types of Charts and Equations

    The following types of chart exist in the IMPC portal from the IMPC:

    1. Categorical Bar Graphs
    2. Unidimensional Scatter and Box Plot Graphs
    3. Time Series Graphs
    4. Pie Graphs graphing viability
    5. ABR graphs showing auditory brain stem response


    Categorical Bar Graphs

    Categorical charts contain data where an observation can be categorised into one of two or more groups e.g. Abnormal Eye or Normal Eye. Charts are presented as bar charts with a table underneath. If IMPC data is available this will be displayed (see statistics help for more information).

    Unidimensional Scatter and Box Plot Graphs



    Where an observation can be measured on a continuous basis (e.g. red blood cell counts or tail length), we display them in a mixed box and scatter plot. The first columns contain box plots for Wild Type (control), Homozygote then Heterozygote mutants for female, then the columns representing males. The second set of columns contains scatter plots for the same sets of data. Hover over the box in the chart to see the basic statistics for that set of data.

    When the data for a parameter is collected at various points in time, a scatter plot shows each data value on the y-axis and the date/time the data was collected on the x-axis.

    Below the chart is a table showing the output of the statistical test used to determine if this data is statistically significant:


    In the top left of the table is the global P value used to determine if this is a statistically significant result.
    The Classification column displays the effect of sexual dimorphism on this association (sexual dimorphism is the phenomenon when the genotype affects the sexes differently). The possible results are:

    No significant change
    The effect is not statistically significant
    Cannot differentiate genders
    For the measured parameter, there is a significant effect, but there is not enough statistical power to determine sexual dimorphism
    Both genders equally
    For the measured parameter, both sexes are affected equally
    Female only
    For the measured parameter, only the females are affected
    Male only
    For the measured parameter, only the males are affected
    Different effect size, females greater
    For the measured parameter, there is an effect on males but the size of the effect on females is greater.
    Different effect size, males greater
    For the measured parameter, there is an effect on females but the size of the effect on males is greater.
    Female and male different directions
    For the measured parameter, the effect on one sex is increased while the other sex is decreased.
    If phenotype is significant it is for the one genotype tested
    For the measured parameter, there was no data for one of the sexes, so sexual dimorphism cannot be determined.

    The more statistics link at the bottom of the table displays additional output related to the statistical method.

    Time Series Graphs

    Where an observation can be measured as a time series (e.g. mean blood glucose concentration), we display the data in a line chart and scatter plot. The line chart will contain lines for wild-type and mutant data for female and for males. The data points displayed are the mean of all data collected at that timepoint and the whiskers indicate standard deviation. Hover over the points to see basic statistics about the data.

    Pie Graphs

    Pie graphs are used to display the results of the primary viability screen. The screen is used to assess the postnatal viability, sub-viability, and lethality of homozygous mice during cohort production.

    ABR Charts

    Auditory Brain Stem Responce data is plotted in the context of the whole serie of ABR measurements, as opposed to plotting each parameter separately. We plot data from the following parameters: click, 6kHz, 12kHz, 18kHz, 24kHz, 30kHz, where the click is separated from the rest of the data. For each parameter we plot the mean of it's respective measurements. If one parameter does not have any points it means no data is available.