Interpreting Gene Expression Data Query Results
Interpreting Gene Expression Data Query Results
This help document answers the following questions:
See also the MGI Glossary for unfamiliar terms and acronyms.
The Gene Expression Database (GXD) is designed to integrate many different types of endogenous gene expression data from the mouse in formats appropriate for comprehensive analysis.
To learn more about GXD and how we acquire data, please see About GXD.
At the top of the Gene Expression Data Query - Summary report is a line of information about the number of expression assays or results found. Beneath this is the table with the query summary results.
TopThe table of results contains a row for each item matching your query. Expression information is contained in assays. Each assay contains some number of experimental results. Query results return either by Assay or by Assay Results.
If your search scope equals assays, the query summary contains the following fields:
Result Details The word data links to detailed expression results; the MGI accession ID of the assay (useful for searching purposes) appears in parentheses. If a camera icon appears, expression data are supported by images such as those from Northern and Western blots and immunohistochemistry and in situ tissue sections. Gene Symbol of the analyzed gene, linked to its MGI marker detail record. Assay Type Name of the assay used (e.g., immunohistochemistry, Northern blot, RNA in situ, and so on). Reference J number (MGI identifier) and short format citation for this reference linked to its MGI reference detail report.
If you return by Assay Results, the query summary contains the following fields:
Top
Result Details The word data links to detailed expression results; the MGI accession ID of the assay (useful for searching purposes) appears next in parentheses. If a camera icon appears, click data to view associated image(s) and assay details. Gene Symbol of the gene assayed for, linked to its marker detail record. Assay Type Name of the assay used (e.g., immunohistochemistry, Northern blot, RNA in situ, and so on). Mutant Allele(s) If the specimen is a mutant, the allele pairs describing the mutant genotype appear in this field. Age Age of the specimen used in the assay. Age annotation abbreviations are:
E Embryonic day P Postnatal or postnatal day P w Postnatal week P m Postnatal month P y Postnatal year P adult Postnatal adult P newborn Postnatal newborn Structure Structure examined in the assay. Given as a Theiler stage and anatomical structure name, linked to The Mouse Anatomical Dictionary Browser - term detail report showing the structure in the anatomical hierarchy. Detected? Yes or No, depending on the presence or absence of a signal in the structure.
An assay detail record provides a brief description of the assay performed, the probe used in the assay, and a tabular representation of the experimental data obtained. The information presented in the table varies depending on assay type. In all cases, the following fields are part of the detail record:
Top
Field Description Reference J number, the MGI reference identifier, linked to the reference detail, and short format citation. Assay Type Name of the assay type used. MGI Accession ID MGI accession ID for the assay. Gene symbol Symbol of the gene assayed, linked to its marker detail record. Gene name Full name of the gene assayed. Modification Date Date the assay was last modified.
The description for assays that use nucleotide probes may include the following additional fields:
Top
Field Description Reporter If the assay type is in situ reporter (knock-in), the name of the reporter gene. Probe Name of the probe used, linked to its detail record. Probe preparation Brief description of the probe material used and preparation details. Visualized with Technique used to visualize the probe. Assay notes If present, notes about the assay that the curators feel are necessary to interpret the results: for example, a description of the experimental conditions.
The description for assays that use antibodies may include
the following additional fields:
Top
Field Description Reporter If the assay type is in situ reporter (knock-in), the name of the reporter gene. Antibody Name of the antibody used, linked to the antibody detail record in the database. Detection System Method used to visualize the antibody. Assay notes If present, notes about the assay that the curators feel are necessary to interpret the results: for example, a description of the experimental conditions.
The description for in situ reporter (knock in) assays that use direct detection includes the following additional fields:
Top
Field Description Reporter Name of the reporter gene. Direct Detection Indicates that the expression of the reporter gene was detected using a direct method, such as fluorescence or using an enzymatic substrate. Assay notes If present, notes about the assay that the curators feel are necessary to interpret the results: for example, a description of the experimental conditions.
Data records also present details of experimental results in a tabular format that varies depending on assay type.
For gel assays, a Gel Data section is provided. Note that the information for each gel lane runs horizontally on the display. If the reference includes an image of the gel, the figure name appears in the Image field above the table. If a camera icon appears, the label links to a detail report containing an image of this gel. Notes may appear below the table, providing further information about the tissues analyzed, age of the specimens, or details about the bands.
| Lane | Sample Information: Age | Sample Information: Structure | Bands | Other Sample Information: Amount | Genetic Background | Mutant Allele(s) | Sex |
| Field | Description | ||||||||||||||
| Lane | Each lane is represented as a row in the table. The Lane label is given as "Lane #," unless the authors specify labels for the lanes. | ||||||||||||||
| Sample Information: Age | Age of the specimen used in the assay. Whenever possible, the age annotations are normalized according to the following conventions: noon of the day on which the vaginal plug is found is counted as embryonic (E) day 0.5. Therefore, e.g., if an author refers to the day on which the plug is found as E0, we add 0.5 to the age value(s) listed in the paper and the comment Age normalized so that noon of plug day = E0.5 to the record. If the staging criteria are not described in the paper, we annotate to the ages given by the authors and may add the comment Age of embryo at noon of plug day not specified in reference to the record. The abbreviations for age annotation are as follows:
| ||||||||||||||
| Sample Information: Structure | Structure examined in the assay. Given as a Theiler Stage and anatomical structure name, linked to the The Mouse Anatomical Dictionary Browser - term detail report which shows the structure in the anatomical hierarchy. | ||||||||||||||
| Bands | Each band in the assay results is represented by a column. If the gel is a nucleic acid gel, the size of the band (if reported) is given in bases (b), base pairs (bp), or kilobases (kb). If the gel is a protein gel, the size of the band (if reported) is given as Daltons (Da) or kiloDaltons (kDa). There may be multiple bands per assay.
The strength of the signal is reported. Possible values include:
*Present appears if expression is reported as detected but the author did not specify the level. | ||||||||||||||
| Other Sample Information: Amount | Sample amount, if given, in microgram units and RNA type (total or poly A+). For RT-PCR reactions, the sample amount is the quantity of RNA used for the reverse transcription reaction. This field is not used for Westerns. | ||||||||||||||
| Genetic Background | Strain information for the specimen, if specified. Use of involves: in the annotation indicates that the strains listed (separated by asterisks) contributed to the genetic background of the specimen; additional unspecified strains may also be part of the specimen's genetic background. Either: appears when the authors use more than one genetic background in a reference but do not specify which one is the background of the specimen. | ||||||||||||||
| Mutant Allele(s) | If the specimen is a mutant, the allele pairs describing the mutant genotype appear in this field, linked to the Phenotypic Allele Detail report. | ||||||||||||||
| Sex | Sex of the specimen, if specified. |
Note: We do not include information from gel lanes containing material from transgenic mice (i.e., animals containing randomly inserted transgenes), cultured specimens, non-mouse species, assay controls, animals that have been manipulated (either by injection of most substances or surgical procedures), or molecular weight markers.
TopThe detail record for RNA in situ, immunohistochemistry, and in situ reporter (knock in) assays includes a section describing the specimens used in the experiment and a section describing the experimental results.
In the tabular display, each column represents a specimen discussed in the reference. The attributes of the specimen appear as rows in the table. The heading in each column is linked to the results obtained for each specimen. Notes providing additional details about the specimen may appear below the table.
Top
For each specimen, a results table appears with the following columns in the display.
Top
Field Description Structure Structure examined in the assay. Given as a Theiler stage and anatomical structure name, linked to The Mouse Anatomical Dictionary Browser - term detail report which shows the structure in the anatomical hierarchy. Level Refers to the strength of the signal. Possible values include:
- Absent
- Ambiguous*
- Moderate
- Not Specified*
- Present*
- Strong
- Trace
- Very strong
- Weak
*Present appears if expression is reported as detected but the author did not specify the level. Not specified is used when the authors do not report whether a gel band is present or absent. Ambiguous is used when the curators cannot discern from the authors’ description whether expression is present or absent.
Pattern Indicator of expression pattern as specified by the author. Possible values include:
- Diffuse
- Graded
- Non-uniform
- Not specified
- Patchy
- Punctate
- Regionally restricted
- Scattered
- Single cells
- Spotted
- Ubiquitous
- Uniform
- Widespread
Note Link to note containing additional information pertaining to the assay result. If present, the notes appear below the results table. Image Figure illustrating the result in the reference. If a camera icon appears, the figure label links to a detail report containing an image of the original data.
Whenever possible, the text descriptions of expression patterns are complemented by digitized images of the original expression data. Images appear on detail reports containing the following fields above the image:
Field Description Reference J number, linked to the reference detail, and short format citation of the reference the image is derived from. Figure Figure number/title of the image in the reference. MGI Accession ID MGI accession ID of the image.
The following fields appear below the image:
Top
Field Description Caption Notes that the curators feel are necessary to orient users when viewing the image. Copyright Copyright statement for the images, in a format specified by the publisher of the reference. Associated Assays
- Listing of image panes referenced in the database.
- Each listing includes the pane label; the MGI accession ID of the assay that the pane was referenced in, linked to the assay record; and the marker (in parentheses) whose expression was examined in the assay, linked to its marker detail report.
- In some cases, the listing may include a link to the spatial mapping at EMAGE for expression data in the pane.
Other Database Links When present, this field displays links to information about the image in databases other than MGI (e.g. GenePaint)
The Your Input Welcome button, located at the top right of your screen, appears as part of the detailed query results. Clicking the button brings up a dialogue box to allow you to submit your comments on the data you are viewing to our User Support staff. They will review your comments and take appropriate action.
Top