Querying the ATLAS-D2K Data Browser

This section describes many ways to search ATLAS-D2K data:

Table of Contents

What is a data record in ATLAS-D2K?

For ISH and IHC specimen data, a data record contains the expression data for a single gene, assayed with a defined probe in a single mouse strain of a single mouse sex at a single stage or time in development. Sex can be unknown (e.g. RID=N-GNB0).

For microarray, a data record encompasses the expression data for many genes sampled from a single stage or time in development. Sex can be unknown (e.g. RID=R-ZX6Y) or both. Each record relates to a single sample taken from a single microarray series within the database. So if you search by gene, you’ll see all microarray entries that contain that gene on the chip.

Query by Gene

Enter a gene symbol/name (or synonym) in the search box on the homepage (https://www.atlas-d2k.org) or by using the top-level menu navigation (Data > Gene).

The results include records that contain information about the expression of the gene or genes of interest. The column “Available Expression Data” indicates the presence of Expression Scoring, Array Data or Imaging data from specimen (in situ, etc). The Imaging column includes representative thumbnails of the imaging data.

In the left sidebar of the results, you may filter results further by these categories:

  • Gene Symbol

  • Species

  • Synonyms

  • Any Expression Data (yes, no)

  • Imaging Data (yes, no)

  • Scored Expression Data (yes, no)

  • Array Data (yes, no)

  • scRNA-Seq Visualization (yes, no)

  • mRNA-Seq Visualization (yes, no)

  • Synonyms

  • MGI Symbol

  • Scored Anatomical Region

  • Specimen Assay Type

  • Antibody Tests

The search automatically assumes a ‘wildcard’ at the end of the search string; therefore, typing in ‘uro’ will search for words/symbols beginning with ‘uro’, e.g. urothelium, urogenital, uroplakin, etc.

Multiple genes (Batch Query)

To search for multiple genes, use the Batch Query method. Use the search method described above but enter multiple genes separated with a pipe character ( | ) with no spaces in between. For example:

APT6|COX1|Six2

This list may contain a mixture of different terms (e.g. MGI accession IDs and MCBI Gene Symbols).

Query by Anatomy

From the menu navigation, go to Data > Anatomy and choose either Anatomy: Facet Search or Anatomy: Tree View.

Searching by Anatomy Tree (for mouse anatomy)

Go to the Anatomy Tree view.

Navigating to the anatomy tree

This option provides a tree structure view of anatomical terms that conform to the GUDMAP Ontology.

Start by choosing an Age Stage in the dropdown field and then typing an anatomical region in the search field.

In the example below, we chose “All Stages” and typed “prostate”. If there are results, the tree will highlight corresponding term(s) and scroll down to the first instance:

image alt text

Click a term to go to the corresponding Anatomy record page (we have more details on this page in the next section):

Anatomy page for prostate gland

You can reach the Anatomy faceted search page here.

This is the Anatomy section of the Data Browser where you may use the left filter sidebar to choose or search for anatomy regions by Name or ontology IDs (ie, EMAPA:18976). Click the View icon of the row you’re interested in to view the corresponding Anatomy record page (see below).

Screenshot of the Anatomy faceted search

Anatomy record page

Below is an example of an Anatomy record page for the term “cortical renal tubule”.

Example of an anatomy page

On the Sections sidebar to the right side of the page, you’ll see a list of available data including the following types:

  • Specimen Expression Rollup

  • Anchor Gene Rollup

  • Marker Gene Rollup

  • Gene List Rollup

  • Mouse Allele Expression

The numbers to the right of the names indicate how many instances of these types of data are available.

Search for genes annotated with expression present, uncertain or not detected

You can search sequencing data for annotations on expression strength.

From an Anatomy record page, choose “Specimen Expression Rollup” in the Sections list. This table includes entries that include annotated in situ expression data and microarray data.

  • For Specimen (ISH/IHC) that contain either a direct annotation for the anatomical term specified (whether it is present, uncertain or possible) or an inferred annotation for the anatomical term (see below).

    Each entry includes the relevant symbol for the gene expressed in the queried structure. Symbols are the current standard gene symbols (see NCBI). To better understand the context of your results please see the tutorial on genitourinary development.

  • For Microarray where the anatomical term specified is the sample material or where sub-components of the anatomical term have been used as sample material.

    For example, using the term ‘maturing nephron’ for the query will return database entries where the sample was the ‘early proximal tubule’ and entries where the sample was ‘maturing renal corpuscle’. Both structures are part of the maturing nephron.

Challenges on searching by anatomical terms

Structures are often referred to with a variety of different terms. The predictive text in the “Tissue (Anatomical Source)” filter on the Specimen search page will help you enter the correct term.

However, some structures have common names that begin with different text from the ontology name. For example, proximal tubule is represented by the term renal proximal tubule in the ontology.

You can easily find the ontology term for a structure by viewing the interactive anatomy ontology tree on the left side of the Boolean Anatomy Search page. This tree is supported by a text string search that will find terms containing a given string. For example, typing proximal in the “find anatomy component” box will highlight renal proximal tubule in the tree.

Queries can be performed for multiple components by entering terms separated by a pipe | character with no space in between (e.g. kidney|ovary). Predictive text is available only for the first term in the list but other valid ontology terms can be added by typing on, using the pipe character to separate terms. Queries with multiple terms are treated as A OR B OR C.

Inferred annotation

We support inferred annotation, that is, we indicate if a region inherits the annotation of a related region.

Suppose, for example, the anatomical term “superficial cellular layer” has been annotated as expression present for a particular gene.

As a consequence, the anatomical term “urothelium” has the inferred present annotation (even though it has not been annotated directly) because “superficial cellular layer” is a part of the urothelium. Equally, if urothelium was annotated as not detected then its parts, including superficial cellular layer would have the inferred not detected annotation.

The original annotations and original expression images are displayed on the page for the corresponding database entry.

The Boolean Anatomy Search allows complex queries to be constructed to search for gene expression based on selected anatomical structures.

The search allows combinations of structures and developmental stages and different combinations of expression found to be present, not detected and uncertain. The search can be applied to a combination of structures or just to one structure.

For example, to retrieve only genes expressed in a structure, or to compare expression in the same structure at different stages.

For more details, please go to the Boolean Anatomy Search page.