How to Search Phenotypes
Simply start typing in the Phenotype Search box. The default setting for a simple phenotype search is search ‘All’. Automated text matching will suggest terms from curated phenotypes that use anatomy terms, Xenopus gene list, and Disease names. Either mouse over and click to select a suggested term from the auto-suggest menu or click the Search button. Enter any of these words or partial words:
- Gene symbols (e.g., pax3, sox10, dyrk1a), or partial gene symbols (e.g., pax, sox)
- Anatomy (e.g., eye, pronephric kidney, heart, blastopore)
- GO - Biological Processes (e.g., gastrulation, brain development, neural tube closure, swimming behaviour)
- NBO - neurological behaviours (predation avoidance)
- Disease names (e.g., cataract, ciliopathy, congenital heart disease, syndromal intellectual disability)
Too many results? Too few results?
Choose a Category from the options on the left, then enter your query word and hit enter/return or search button, or you can mouse down to choose a match from the drop down suggestions. This will filter all results to just those matches in the chosen category.
Gene (manipulated): Use official gene symbols only (e.g., tbxt, pitx1, lhx1) to find:
- Anatomical phenotypes where your gene was manipulated (i.e., loss of function via CRISPR or morpholino, or gain of function via mRNA injection)
- Expression Phenotypes where your gene was manipulated and other genes were assayed
- Diseases Phenotypes associated with a genes loss of function or gain of function
Gene (assayed):
- Expression Phenotypes where your gene was assayed.
- Manual Expression - expression phenotypes from in situ hybridization or immunohistochemistry assays
- Computational Expression - expression phenotypes from high throughput sequencing (e.g., RNA-Seq, ATAC Seq)
Anatomical Phenotype:
- all phenotypes affecting an organ, tissue or cell types, and impacting a GO Biological Process (e.g., apoptosis, neural tube closure, gastrulation, tail regeneration) or behaviour (e.g. swimming)
Expression Phenotype:
- all phenotypes where gene expression has changed in a specific cell type, tissue or organ
- Search with a gene symbol or an anatomy term.
Example results:‘decreased expression of epha4.L in pronephric kidney’‘increased expression of gsc in dorsal marginal zone’
- This expression phenotype could either manually or computationally curated.
- Manual Expression - expression phenotypes derived from in situ hybridization or immunohistochemistry assays, or any high throughput sequence data that is manually curated from a figure in a paper.
- Computed Expression - expression phenotypes derived from high throughput sequencing experiments (e.g., RNA-Seq, ATAC Seq) that have been curated by Xenbase from GEO [Gene Expression Omnibus], an NCBI database.
- In X. laevis, the gene will be shown as the ‘.L’ homeolog by default, unless specified as the ‘.S’ homeolog by the authors.
Disease
- search using Disease Ontology (DO) terms to find Xenopus disease model phenotypes.
Troubleshooting
- If no phenotypes are returned for a specific Disease name, try a search using a gene symbol related to that disease: e.g. dyrk1a, an autism risk gene associated with
intellectual disability
in human patients, has phenotypes ‘abnormal multiciliated cells’, ‘abnormal brain morphology’, ‘abnormal telencephalon’ and ‘increased amount of aurka expression in the brain’ (see
XB-ART-57038, Willsey et al. 2020
), while these phenotypes may be associated with autism and intellectual disability.
- To find genes associated with a disease, see the OMIM or DO Disease Pages which collate all the Xenopus genes and literature associated with each disease.
- Search diseases here:
disease.do?method=search&searchIn=10
- Use up-to-date gene symbols to find phenotypes (e.g.,
tbxt, not t or brachyury; en1 not engrailed; gsc not goosecoid).
- Legacy gene symbols are listed as synonyms of Xenbase gene pages.
- Partial gene symbol (e.g., pax, bmp, sox, slc, fox) will return all phenotype matches for all members of that family
- Phenotype search is currently limited to a single search term, so you cannot enter gene lists or use AND or NOT.