UCSC Xena and Cancer Genomics Browser

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Welcome! Please feel free to ask questions, comment and recommend new features for UCSC Xena (http://xena.ucsc.edu/).

Note all content here is moderated. It may take up to 24 hours for your content to be posted.

If you want to hear the latest about new data and features, please subscribe to our announcements-only mailing list here: http://xena.ucsc.edu/#whatsnew. You can also follow us on twitter at https://twitter.com/UCSCXena.

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Sandhya, Mary Goldman2

Apr 11

Constructing PPI, GGI, and Coexpression Networks from TCGA Data

Hi Sandhya, I'm afraid we're not funded to advise on how to extract PPI, GGI, and

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Constructing PPI, GGI, and Coexpression Networks from TCGA Data

Hi Sandhya, I'm afraid we're not funded to advise on how to extract PPI, GGI, and

Apr 11

Racha Hosni, … Mary Goldman4

Apr 8

Help with: "None of these fields are available on all selected datasets."

Hi Katarina, I am able to visualize "hsa-miR-675" for GDC Head and Neck https://xenabrowser

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Help with: "None of these fields are available on all selected datasets."

Hi Katarina, I am able to visualize "hsa-miR-675" for GDC Head and Neck https://xenabrowser

Apr 8

Karen Vara, Mary Goldman2

Apr 3

Doubts about normal tissues in TCGA

Hello, I would recommend contacting the GDC about this (https://gdc.cancer.gov/support) or the

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Doubts about normal tissues in TCGA

Hello, I would recommend contacting the GDC about this (https://gdc.cancer.gov/support) or the

Apr 3

Racha Hosni, Mary Goldman2

Mar 27

Normal vs. primary tumor samples

Hi Racha, I recommend adding the column '_PATIENT' to your view. This will allow you to

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Normal vs. primary tumor samples

Hi Racha, I recommend adding the column '_PATIENT' to your view. This will allow you to

Mar 27

Federico Nichetti, Mary Goldman2

Feb 20

download transcript TPMs?

Hi Federico, The Transcript Browser is designed to compare one group of donor samples to another

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download transcript TPMs?

Hi Federico, The Transcript Browser is designed to compare one group of donor samples to another

Feb 20

Vladimir Wischnewski, Mary Goldman3

Feb 13

Counting overlapping reads

Hi Mary, Thank you very much for your quick reply. This info is unfortunately not provided on the

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Counting overlapping reads

Hi Mary, Thank you very much for your quick reply. This info is unfortunately not provided on the

Feb 13

Karen Vara, … Mary Goldman4

Feb 12

We have a doubt about the term "primary_therapy_outcome_success"

Hi Jazmin, If you are unable to find the information in the paper and supplementary information then

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We have a doubt about the term "primary_therapy_outcome_success"

Hi Jazmin, If you are unable to find the information in the paper and supplementary information then

Feb 12

Ashwin Mukund, … Mary Goldman4

Feb 9

GDC-TCGA/Xena Browser Data Differences

Hi Augustina, Yes, exactly. The files that we host are from 2019 and underwent different

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GDC-TCGA/Xena Browser Data Differences

Hi Augustina, Yes, exactly. The files that we host are from 2019 and underwent different

Feb 9

Rademaker Gilles, Mary Goldman2

12/20/23

Hi Gilles, Apologies - this is expected since CCLE does not want UCSC Xena to provide the underlying

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Hi Gilles, Apologies - this is expected since CCLE does not want UCSC Xena to provide the underlying

12/20/23

Ziyuan Zhao, Mary Goldman2

11/27/23

KM plot grouped by sample names

Hello, Yes, you can run a KM plot where your subgroups are defined however you choose. For an example

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KM plot grouped by sample names

Hello, Yes, you can run a KM plot where your subgroups are defined however you choose. For an example

11/27/23

Hemasri Sai, Mary Goldman2

11/20/23

Details about samples from TCGA KIRC data

Hi Hema, These 311 samples contain both tumor and solid tissue normal from a number of individuals.

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Details about samples from TCGA KIRC data

Hi Hema, These 311 samples contain both tumor and solid tissue normal from a number of individuals.

11/20/23

Sandhya, Mary Goldman2

10/30/23

How to generate PPI Network work from String data base

Hello, Unfortunately Xena does not calculate PPI networks. The paper you mention in your email I

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How to generate PPI Network work from String data base

Hello, Unfortunately Xena does not calculate PPI networks. The paper you mention in your email I

10/30/23

Sandhya, Mary Goldman4

9/26/23

Multi omics data

Hello, In our tutorials we point folks to these two resources: https://www.ebi.ac.uk/training/online/

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Multi omics data

Hello, In our tutorials we point folks to these two resources: https://www.ebi.ac.uk/training/online/

9/26/23

Alan Aboudib, Mary Goldman2

9/5/23

ICGC version used for PCAWG

Hi Alan, I believe the information you are looking for is in the Nature publication: https://www.

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ICGC version used for PCAWG

Hi Alan, I believe the information you are looking for is in the Nature publication: https://www.

9/5/23

Liuling Xiao, Mary Goldman2

8/28/23

GDC MMRF-COMMPASS

Hi Liuling, Looking around I found these web pages related to the MMRF COMMPASS study: https://gdc.

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GDC MMRF-COMMPASS

Hi Liuling, Looking around I found these web pages related to the MMRF COMMPASS study: https://gdc.

8/28/23

Genaro Camele, Mary Goldman4

8/8/23

Get all the samples and probes of a dataset

Hello, Sorry, our API is designed to give users slices of the data, not the whole dataset. That said,

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Get all the samples and probes of a dataset

Hello, Sorry, our API is designed to give users slices of the data, not the whole dataset. That said,

8/8/23

Rademaker Gilles, Mary Goldman4

8/7/23

GSEA analysis not possible error subgroup 1 has no samples

HI Gilles, I wanted to let you know that this has been fixed. You should no longer need to change

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GSEA analysis not possible error subgroup 1 has no samples

HI Gilles, I wanted to let you know that this has been fixed. You should no longer need to change

8/7/23

Ping-Hung Chen, Mary Goldman3

7/21/23

Not able to use Single cell browser

Hi Ping-Hung, The single-cell browser should now be back up. Let us know if you run into any issues.

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Not able to use Single cell browser

Hi Ping-Hung, The single-cell browser should now be back up. Let us know if you run into any issues.

7/21/23

Daniel Nicorici, Mary Goldman2

6/29/23

Feature request -> add "auto threshold" for Kaplan-Meier plots

Hi Daniel, Great suggestion. Thank you so much for the idea and all your links! I will add this to

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Feature request -> add "auto threshold" for Kaplan-Meier plots

Hi Daniel, Great suggestion. Thank you so much for the idea and all your links! I will add this to

6/29/23

Pierre-Alex Laval, Mary Goldman2

6/27/23

Difference in DGE and GSEA ?

Hi PA, For both the Differential Gene Expression and the GSEA analyses, there are two options for

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Difference in DGE and GSEA ?

Hi PA, For both the Differential Gene Expression and the GSEA analyses, there are two options for

6/27/23

Keon Abedi, Mary Goldman2

6/15/23

Not able to download a local Xena Hub?

Hi Keon, Thank you for reporting this! It should now be fixed. The words 'download & run a

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Not able to download a local Xena Hub?

Hi Keon, Thank you for reporting this! It should now be fixed. The words 'download & run a

6/15/23

Pierre-Alex Laval, Mary Goldman4

6/14/23

Show GSEA graph for the sets below the 50 firsts ?

Hi Pierre, Yes, please do come back if you have any difficulties. Have a great day too! Best, Mary --

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Show GSEA graph for the sets below the 50 firsts ?

Hi Pierre, Yes, please do come back if you have any difficulties. Have a great day too! Best, Mary --

6/14/23

Piyal saha, Mary Goldman2

6/14/23

Difference between Normal tissue and Solid Tissue normal

Hi Piyal, There are two sources of normal tissue in the TCGA TARGET GTEX dataset: matched normal from

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Difference between Normal tissue and Solid Tissue normal

Hi Piyal, There are two sources of normal tissue in the TCGA TARGET GTEX dataset: matched normal from

6/14/23

Khushbu Patel, … Holly Beale3

6/14/23

Tumor Compendium v11 Public PolyA (April 2020) - hg19 or hg38?

Hi Kushbu- hg38. Details here: https://github.com/UCSC-Treehouse/pipelines/blob/master/CGL_TOIL_RNA-

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Tumor Compendium v11 Public PolyA (April 2020) - hg19 or hg38?

Hi Kushbu- hg38. Details here: https://github.com/UCSC-Treehouse/pipelines/blob/master/CGL_TOIL_RNA-

6/14/23

YH Dai, Mary Goldman2

5/3/23

Hello, The data is mapped to hg38, similar to other data we have from the GDC. Can you tell me more

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Hello, The data is mapped to hg38, similar to other data we have from the GDC. Can you tell me more

5/3/23

YH Dai, Mary Goldman2

4/26/23

GDC pancancer ATAC-seq data

Hello, The column headers are the samples. The rows are the ATAC-seq peaks. You can view the mapping

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GDC pancancer ATAC-seq data

Hello, The column headers are the samples. The rows are the ATAC-seq peaks. You can view the mapping

4/26/23

Josh V, Mary Goldman2

4/19/23

What was the Kallisto command?

Hi Josh, I would recommend looking at the publication associated with this dataset for the full

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What was the Kallisto command?

Hi Josh, I would recommend looking at the publication associated with this dataset for the full

4/19/23

4/19/23

What stage cancer is the primary tumour in the GDC PRAD prostate cancer dataset...? TIA Jessica Mace

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What stage cancer is the primary tumour in the GDC PRAD prostate cancer dataset...? TIA Jessica Mace

4/19/23

Devipriya Raju, Mary Goldman2

3/15/23

Couldnt access the gene expression data of TCGA PANCAN

Hi Devipriya, You need to enter a gene, list of genes, or a chromosome position in order for the Done

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Couldnt access the gene expression data of TCGA PANCAN

Hi Devipriya, You need to enter a gene, list of genes, or a chromosome position in order for the Done

3/15/23

3/15/23

unread,

3/15/23

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