GUDMAP database - Query help page
All queries will return a list of GUDMAP entries. What is a GUDMAP entry?
For ISH and IHC, entries contain 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. GUDMAP:9683).
For microarray, entries encompass the expression data for many genes sampled from a single stage or time in development. Sex can be unknown (e.g. GUDMAP:7077) or both. Each entry relates to a single sample taken from a single microarray series within the database. So if you search by gene you'll get returned all microarray entries that contain that gene on the chip.
Contents
- Querying by gene
- Querying by anatomy
- Querying by accession number
- Querying by function
- Advanced Anatomy Query
Query > Gene
The Query > Gene text box can be used to return GUDMAP entries that contain information about the expression of the gene or genes of interest.
Genes can be searched for using the following terms:
- Gene Symbols/Names (and synonyms)
- MGI, Ensembl and MTF accession IDs
By clicking on 'options' next to the text box, restrictions can be applied to the search criteria:
- The operators 'starts with', 'equals' or 'contains' can be applied.
- The search can be restricted to an individual Theiler stage.
- The output can list 'all entries' or 'annontated entries only'.
The default is 'starts with', ALL Theiler stages and list all entries.
NOTE: When entering an accession ID be sure to use the full name (e.g. MGI:98957 or ENSMUSG00000036856) - searches will only be success if an exact match is found, even if the 'starts with' operator is used.
Multiple genes
It is possible to search for multiple genes in two ways. Firstly by entering terms into the Query > Gene text box as a semicolon (;) separated list. This can contain a mixture of different terms (e.g. MGI accession IDs and Gene Symbols).
Secondly by clicking on options and using the batch query tool to upload a file containing a list of gene symbols. The batch query will accepted data as either tab-delimited or newline-delimited csv file or plain text file - the batch query will only accept query by gene symbol.
Query > Anatomy
The Query > Anatomy text box accepts anatomy terms contained within the Mouse Genitourinary System Anatomy Ontology. The ontology is described in more detail in the ontology resources page, with links to tables containing the full ontology.
The ontology can also be easily viewed on the Advanced Query page where it is presented on the left-hand side of the page as a tree menu. Anatomy terms can be copied and pasted (omitting the TS stage range) from there into the Query > Anatomy text box on the main query page.
The result of this type of query will be a list of GUDMAP entries:
- For 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.
- For Microarray - where the anatomical term specified is the sample material as well as microarray entries where subcomponents of the anatomical term have been used as sample material
Queries can be performed for multiple components by entering terms as a semicolon separated list (e.g. 'kidney; ovary').
Inferred annnotation
In the example below the anatomical term 'superficial cellular layer' has been annotated as 'present'. As a consequence, the anatomical term 'urothelium' has 'inferred present' annotation (even though it has not been annotated directly) because 'superficial cellular layer' is a child term of 'urothelium'. Equally, if 'urolthelium' was annotated as 'not detected' then its child terms, including 'superficial cellular layer' would have 'inferred not detected' annotation.
Query by accession ID
The Query > Accession ID text box will accept a variety of different accession IDs and will return all GUDMAP entries that contain information about the expression relating to the accession ID.
Accession ID's supported by GUDMAP:
- GUDMAP entry ID's (e.g. GUDMAP:8200, GUDMAP:7720). The ID must contain the 'GUDMAP:' prefix.
- Ensembl ID (e.g. ENSMUSG00000016458). The ID must contain the 'ENSMUSG' prefix.
- MGI ID (e.g. MGI:98968). The ID must contain the 'MGI:' prefix.
- MA probe ID (e.g. maprobe:4427). The ID must contain the 'maprobe:' prefix.
- MTF accession ID's
Queries using multiple accession IDs can be performed by entering terms as a semicolon (;) separated list (e.g. GUDMAP:7200;MGI:98957).
NOTE:when searching using an ID other than GUDMAP ID only in-situ (ISH & IHC) entries will be returned.
Query by function
The query-string entered into the Query > Function text box will be used to search GO (Gene Ontology) terms. The list of GO terms can be accessed via the Gene Ontology (GO) website. It is also possible to view these terms at MGI - via this link.
The query-string entered into the text box will be used to search the GO ontology for occurences of this term. It will pick up all GO terms that contain the query-string e.g. if a search is done using 'gonad' GO terms such as gonad development and gonad morphogenesis will be found. For each of the GO terms found a check is done to find all gene products annotated with these terms. A nice explanation of the methods and types of annotation used by GO is the GO Evidence Decision Tree.
The list of gene products gives a list of gene symbols that can then be used to search the GUDMAP database find entries that contain information about the expression of these genes.
NOTE: Searching by function will only return ISH or IHC entries.
The Advanced Query page is a boolean query that allows complex queries to be constructed to seach for gene expression based on selected anatomical structures.
For details on using the Advanced Query please go to the Advanced Anatomy Query Help Page.