Xenopus Phenotypes on Xenbase

1. Xenopus Phenotypes on Xenbase

Xenbase is taking an innovative approach to curate and display phenotypes in Xenopus. Our goal is to make a simple, easy to use interface for researchers to quickly find all relevant phenotypic data on Xenbase. We also want clinicians and non-model organism scientists to be able to find Xenopus phenotypes that relate to and/or phenocopy human disease conditions.

A bit of background on phenotypes:

Xenbase is collecting are 3 different types of phenotypic data:

1. Anatomical phenotypes- such as an abnormal tissue, organ or system.

2. GO phenotypes - abnormal molecular function, biological process or cellular component.

3. Gene expression phenotypes, known as 'Expression as Phenotype', or EaP, where the knock-down, knock-out or overexpression of one gene affects the observable expression of another gene.

For anatomical phenotypes and GO phenotypes, we are developing a Xenopus Phenotype Ontology, the XPO for short, to describe phenotypes arising from a wide range of experimental manipulations and disease modeling. The XPO uses easy to understand anatomy-based and GO term-based phrases (eg. abnormal eye development) as well as clinical terms (e.,g microphthalmia).

EaP statements describe whether expression of 'gene X' is seen in an increased or decreased amount in a tissue or embryo (e.g., pax6 increased amount [in the] retina). EaP phenotypes can be observed in WISH assays or captured from RNA-Seq assays (typically generating a long list of up and down-regulated genes in a tissue or whole embryo). EaP data is informative for pathway and gene regulatory network studies.

This survey will help us understand how you, the Xenopus researcher, would search for phenotypes on Xenbase, and how you might want that data displayed.

Thanks for your input!

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* 1. Without any other leading questions, what would be your first term to search when looking for Xenopus phenotypes? I would search for:

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* 2. What do you think your search workflow would be?

Simple search, then filter if needed

Advanced search at first, then further filtering if needed

Browse all, then filter if needed

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* 3. Which phenotypes are most important to you? (Check all that apply)

Anatomical phenotypes

Gene Expression change phenotypes (EaP)

GO - Biological Process phenotypes

GO - Molecular Function phenotypes

GO - Cellular Component phenotypes

Phenotypes that are linked to human diseases

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* 4. Put another way, I would search for phenotypes that...

copy a human disease phenotype

use specific chemicals or reagent (e.g., LiCl or a morpholino)

are related to a disease

affect a particular tissue

affect a particular gene

affect a particular GO term

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* 5. What types of advanced query options and filters would you want? (Check all that apply)

Tissue assayed (e.g., endoderm, neural crest or heart)

Gene manipulated (e.g., shh, including all morpholino, CRISPR or mRNA experiments)

Reagent used in manipulation (e.g. RA, LiCl, pax8 MO1)

Stage Restrictions (e.g. NF14 - NF18)

Assay type (e.g. ISH, IHC, RNA-Seq )

Manually curated (i.e., phenotypes from research article, curated by Xenbase staff)

Computational results (eg., EaP staements and gene lists from RNA-Seq in GEO)

Gene assayed (e.g., all phenotypes where shh affected)

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* 6. I want my results displayed in these groups... (check all that apply)

phenotype statements with all links to experiments, images, and article(s)

experiment with all phenotype statements

images with all phenotype statements

article(s) with all phenotype statements

Other (please specify)

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* 7. If you have any other comments about phenotypes that you'd like to share- let us know here. We are listening!

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* 8. If you know of a website that shows phenotypes in a way that you really like, please copy the web address URL here and we'll take a look at it.

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* 9. If you want to help us test the new phenotype feature on Xenbase, please tell us who you are and how to contact you. Thank you!

Name:

Institute:

Postion:

Email:

Field of Research:

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* 10. As a Xenopus researcher, we know you use Xenbase! Tell us the things you like the most, anything that we need to fix or do better, or any other stuff we should think about. Again, thank you for your input!

I like this about Xenbase:

You need to fix ....

Here's an idea to think about: