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Gene expression search tips

Xenbase provides a versatile interface for finding Xenopus gene expression data. You can search by one or more of the following criteria:

Looking for a published image? Please see current status of expression data from the literature.


Gene symbol/clone name/affymetrix ID

Genes have been renamed to align Xenopus with human genome nomenclature committee (HGNC) guidelines. We store alternate gene names, or synonyms, in the database and if it is there, your search will find it provided the Search Synonyms box is checked.

Begin typing in the search box to see a dynamically generated list of gene names and synonyms that match your text.

You can also search for expression by clone name or affymetrix ID by selecting that option from the menu at left.

Finally, you can filter your results by selecting a specific Xenopus species from the menu at the far right. You may choose Xenopus, which returns all data or you can select Tropicalis or Laevis only.

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Expressed sequence

You can search for expression patterns based on nucleotide or protein sequence.

In the expandable box, paste your sequence or simply provide a GenBank accession identifier or GI (GenInfo Identifier) number.

Set the E-value in the box to the right (the default is 0.1).

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Developmental stages

With these menus you can search for gene expression during specific stages of development. The stages are based on Nieuwkoop and Faber's Normal Table.

You may specify a single stage or, optionally, a range of stages. In the latter case, any expression observed sometime within that range will be found.

Click the + and - buttons to add and remove stages or stage ranges in your search. Use the Search Any and Search All radio buttons to select the Boolean operator for your search criteria (OR or AND, respectively). Search Any will retrieve expression data for any of the stages/ranges you selected, while Search All will retrieve only those expression patterns that span all of the stages/ranges that you specified.

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Anatomy

You can search for expression patterns in particular tissues or anatomical structures using terms from the Xenopus Anatomical Ontology.

There are two ways to select terms for your search. One option is to choose from a set of 16 commonly used items. In this example, heart and kidney have been checked and they then appear in the Selected Search Terms box to the right.

You can also find terms from the whole anatomical ontology using the suggestion box (below). All terms that match your text will appear in a dynamically generated list in bold text. If your text matches a synonym, it will appear in square brackets after the primary term. If a term has subtypes, they will be listed under that term in plain text (e.g. the types of blood vessels). Choose an item from this menu to add it to your list of search terms.

You can modify your selected search terms by viewing their subparts (if any) and using their checkboxes to include or exclude terms in the search. In the example below, the subparts of heart have been expanded by clicking the [+] icon next to it. By default, all subparts are checked, but you can exclude any from your search by unchecking them. Note that unchecking "heart" will uncheck all of its subparts, while re-checking "heart" will automatically re-check all of its subparts.

To delete a term and all of its parts from your search, click the X icon to its right.

Use the Search Any and Search All radio buttons to select the Boolean operator for your search terms (OR or AND, respectively).

Below the Search Any/All buttons, you can select whether to include successor and predecessor tissues in your search. Successor tissues, selected by default, are tissues and structures that develop from your selected tissues during embryogenesis (e.g. if you select "mesoderm", expression in all mesodermal derivatives will be returned in the search). Predecessor tissues, unselected by default, are tissues from which your selected search items arose. This latter option is a useful way to expand the scope of your search if your original try produces too few results.

To exclude anatomy terms from your expression search query, simply enter your terms in the section marked Exclude These Anatomy Terms:. Terms are entered in the exact same mannar as described above. Genes or clones having expression evidence for the excluded anatomy terms will be filtered out of the result set.

As with the included anatomy terms, you also have the option of including successor and predessor tissues in your excluded anatomy term expression search.

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Experimenter

Enter the name of a researcher or author to find their images from community submissions or the literature.

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Expression pattern, assay, and source filters

If your search is returning too many results, you may wish to use these filters to restrict your results as desired. Uncheck the data types that you want to leave out of your search.

The Expression Pattern options let you filter out results showing "ubiquitous" expression patterns (expression in more than 5 tissues defined from cDNA libraries) or restrict the search to only data mapped to known genes, or only data mapped to clones. Data mapped to clones are linked to Xenbase clone pages containing sequence, library, vector, and supplier information.

The Experimental Assay options are mRNA in situ hybridization, immunohistochemistry, and cDNA libraries.

The Source Type options are community submissions (images directly submitted to Xenbase by the Xenopus community), figures from the Xenopus literature, and images from large-scale in situ screens (Axeldb and XDB3).

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Too many results?

If you are searching for genes expressed in one or more tissues, try the following:
  1. Add a specific stage range to your query. For instance, if you are interested in genes expressed in the heart from stage NF stage 39 to NF stage 44, you would enter this as a stage range to filter out genes showing heart expression outside this range.
  2. Try excluding one or more anatomy terms from your search. For example, if you are interested in genes expressed in the heart but not expressed in the kidney or liver, you would add 'kidney' and 'liver' to the list of excluded anatomy terms.
  3. Select a specific species of Xenopus to search. By deafult, all Xenopus expression patterns are searched, however you have the option of only selecting for either the tropicalis or laevis species.
  4. Apply one or more filters located at the bottom of the expression search form. For example, if you are only interested in receiving genes in your result list, you would uncheck the box marked Mapped To Clones. You are also able to filter results by experimental assay and source type.
If you are searching for genes expressed in a specific development stage or a stage range, try the following:
  1. Add one or more tissues of interest to your search criteria that exist over your desired stage range. For instance, you may only be interested in kidney and bladder expression during NF stage 55.
  2. Try suggestions 2,3 and 4 listed above for searching genes expressed in one or more tissues.

Too few results?

The default options for the expression search results in a fairly non-stringent query. However, if you are not getting that many results from your search, you can try checking the Ubiquitous checkbox in the Filter By: section. Doing so will include genes in your search set that are deemed to show ubiquitous expression (expression in more than 5 tissues defined from cDNA libraries).

If you still are not getting satisfactory results, keep in mind that the Xenbase curators are adding new expression patterns on a daily basis so it is worth re-trying your query at regular intervals. Alternatively, you can Email us with your expression search parameters and we can look into the matter in more detail.


Current status of expression data from the literature

Xenbase reproduces figures and captions from several journals that have granted us the appropriate permissions. We began to include published figures in 2007.

We manually curate all new images with stage and anatomy terms, but we are currently able to annotate those from older publications only on an ad hoc basis. A more complete incorporation of data from older articles and from additional journals is a long-term goal.

Stage and anatomy annotations have been electronically assigned, using a text-matching algorithm, to images that we have not yet curated. This is meant to aid in finding images of interest, but we recommend that you read the image captions to verify stage and anatomy information.

If you have questions or suggestions or would like to submit expression pattern images to Xenbase, please contact us.

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Major funding for Xenbase is provided by the National Institute of Child Health and Human Development, grant P41 HD064556