Tool:XENA: a new tool for cancer researcher developed by UCSC

Question

[ivivek_ngs]

Another tool XENA that comes to the world of Bioinforamatics designed by UCSC. I am not sure if people are aware of it. It is developed recently and I got the notification last evening. Seems to be having a lot of potential for both data visualization and also producing quality images for publication. The paper is not yet out but the mention of the tool was done last year when the update paper of the UCSC Cancer Genomics browser was made for 2015.

The tool has got data from both TCGA and ICGC and is a powerful resource not only for public data comparing and viewing but also one can upload its own data or download the tool locally to a desktop app version and visualize it. The tool is available at the below link

http://xena.ucsc.edu/

The technical doc is here. Am sure it will be a great resource for the researchers and bioinformaticians across the globe. For analysis it also integrates the galaxy as well and if you format your data in a version as mentioned in help docs one can view their data as well. Enjoy and appreciate the work. Hope people would like it.

P.S:

I am not involved in the work. I liked the tool a lot so thought of informing it to the community.

[Shicheng Guo]

very interesting tools, more details can be found here: https://www.biorxiv.org/content/10.1101/326470v5.full

Answer 1

[Istvan Albert]

I have not heard of it yet, went around and attempted to explore it - it looks impressive from technical perspective - a lot work and effort must have gone into it.

Overall though (and this is very typical of software developed by scientists) I felt that the site and its surrounding documentation lacks rationale and evidence for its utility. There should be a few neat examples set up right away.

What is it that we can actually do with it beyond plotting data? What type of discoveries can be made? How does one make use of the visualization? It just seems to assume that once you can visualize it all kinds of interesting observations will be made.

Also from my own experience developing such software, visualization is a very difficult type of service - everyone seems to want things to be displayed a little differently.

[ivivek_ngs]

True that @Istvan Albert, the technicalities and the look of the webtool is quite impressive but I believe visualization these days gives a lot of opportunities to both data scientists and wet lab researcher to make a sense of the data. I am sure when the paper will come out it might be listing out the features in details outlining its scientific capabilities. I believe when you can compare lets say a few set of samples designed in pre customized version as the tool says and map it against the ICGC or TCGA data for visualization , definitely its worth giving a shot. I am not saying it will be very useful at the discovery point of view but yes it will be a powerful resource from the point of building connections or as I must say bring forward certain genes that might make sense when interrogated with large data sets. Also it is a one click tool for wet lab researchers which they always prefer . I give +1 for that .

But it is very evident in this field that visualizations do help us making new observations. Specially when we do not have very high number of samples or resources and need to make the most out of the project. I believe these tools, along with cbioportal really comes to great effectiveness.

Answer 2

[ebrahimiet]

Hi, In downloading the data from Xena UCSC such as the following link: https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/?dataset=TCGA.CHOL.sampleMap%2FmiRNA_HiSeq&host=https%3A%2F%2Ftcga.xenahubs.net How I can get the information regarding samples? such as TCGA-W5-AA2U-01

Thanks Esmaeil

[mary]

Hi Esmaeil,

The columns are the samples. If you're looking for clinical/phenotype information for a sample, I recommend looking at this file: https://xenabrowser.net/datapages/?dataset=TCGA.CHOL.sampleMap/CHOL_clinicalMatrix&host=https://tcga.xenahubs.net

Best,

Mary

Mary Goldman UCSC Xena Browser http://xena.ucsc.edu/