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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Lin lingo, Mary Goldman2

Nov 21

Regarding data discrepancies between different versions:

Hello, For the v18 data, we took clinical data from both the clinical data files on the GDC as well

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Regarding data discrepancies between different versions:

Hello, For the v18 data, we took clinical data from both the clinical data files on the GDC as well

Nov 21

Ghislain Breton, Mary Goldman2

Nov 14

How to idenitfy TCGA dataset generated from rRNA depletion

Hi Ghislain, I would recommend contacting the GDC about this: https://gdc.cancer.gov/support. Best,

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How to idenitfy TCGA dataset generated from rRNA depletion

Hi Ghislain, I would recommend contacting the GDC about this: https://gdc.cancer.gov/support. Best,

Nov 14

CR F, Mary Goldman2

Nov 6

GDC-PANCAN missing files

Hi Carlos, We have recently updated the GDC data and retired the 2019 data you are referencing to

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GDC-PANCAN missing files

Hi Carlos, We have recently updated the GDC data and retired the 2019 data you are referencing to

Nov 6

Donogh O'Brien, Mary Goldman4

Oct 29

GTEX TCGA new recompute available?

Hi Don, Too bad the download possibilities are so limited. And good to know about the TAAs. Thank you

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GTEX TCGA new recompute available?

Hi Don, Too bad the download possibilities are so limited. And good to know about the TAAs. Thank you

Oct 29

Marissa D, Mary Goldman2

Oct 23

Germline data for TCGA Lung Cancer

Hi Marissa, TCGA considers germline data to be protected. UCSC Xena does not host any protected data

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Germline data for TCGA Lung Cancer

Hi Marissa, TCGA considers germline data to be protected. UCSC Xena does not host any protected data

Oct 23

Jacob Neumann, Mary Goldman2

Oct 23

Hi Jacob, The TCGA-GTEx dataset was generated in 2017 using Gencode v23. At this point in time the

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Hi Jacob, The TCGA-GTEx dataset was generated in 2017 using Gencode v23. At this point in time the

Oct 23

Enrique Medina-Acosta, Mary Goldman2

Oct 16

[ucsc-cancer-genomics-browser] GDC-PANCAN.methylation27.tsv and GDC-PANCAN.methylation450.tsv - temporary downtime or inaccessible.

Hi Enrique, We have recently updated the GDC data and retired the 2019 data you are referencing to

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[ucsc-cancer-genomics-browser] GDC-PANCAN.methylation27.tsv and GDC-PANCAN.methylation450.tsv - temporary downtime or inaccessible.

Hi Enrique, We have recently updated the GDC data and retired the 2019 data you are referencing to

Oct 16

Alex Azizi, Mary Goldman3

Oct 8

SNP6 PANCANCER data - which log()? broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena

Dear Mary, Thank you for this detailed and illuminating response! It is really helpful. I will follow

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SNP6 PANCANCER data - which log()? broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena

Dear Mary, Thank you for this detailed and illuminating response! It is really helpful. I will follow

Oct 8

初子斌, Mary Goldman2

Sep 3

The problem of finding data samples

Hello, I believe all healthy TCGA copy number data is considered to be protected data. You will need

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The problem of finding data samples

Hello, I believe all healthy TCGA copy number data is considered to be protected data. You will need

Sep 3

Aug 21

Does single cell Xena have a problem?

Hello, Does single cell Xena (https://singlecell.xenabrowser.net/heatmap/) have a problem? I could

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Does single cell Xena have a problem?

Hello, Does single cell Xena (https://singlecell.xenabrowser.net/heatmap/) have a problem? I could

Aug 21

Özge Yüksel, Mary Goldman2

Jul 18

Accessing and Processing Mature miRNA Data in TCGA BRCA Cohort

Hello, Here is our dataset page for this data (https://xenabrowser.net/datapages/?dataset=TCGA.BRCA.

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Accessing and Processing Mature miRNA Data in TCGA BRCA Cohort

Hello, Here is our dataset page for this data (https://xenabrowser.net/datapages/?dataset=TCGA.BRCA.

Jul 18

Zhicheng Zhou, Mary Goldman2

Jul 15

The issues on CCLE dataset

Hi Zhicheng Zhou, Apologies, CCLE has requested that we only visualize their data. If you would like

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The issues on CCLE dataset

Hi Zhicheng Zhou, Apologies, CCLE has requested that we only visualize their data. If you would like

Jul 15

Joan Frigola Rissech, Mary Goldman2

Jul 1

PCAWG - Duplications size

HI Joan, I would recommend going to the PCAWG publications themselves to answer these questions.

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PCAWG - Duplications size

HI Joan, I would recommend going to the PCAWG publications themselves to answer these questions.

Jul 1

Arpita Mohapatra, Mary Goldman2

Jun 26

DGE analysis on TCGA samples

Good morning, We automatically run DGE on our default datasets, which for most cohorts is not the

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DGE analysis on TCGA samples

Good morning, We automatically run DGE on our default datasets, which for most cohorts is not the

Jun 26

Arpita Mohapatra, Mary Goldman2

Jun 24

internal server error

Hi Arpita, Thank you for reporting this issue. We have fixed it and our DEA should be back up. Let me

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internal server error

Hi Arpita, Thank you for reporting this issue. We have fixed it and our DEA should be back up. Let me

Jun 24

Karen Vara, Mary Goldman2

May 13

Help with: Sample processing (TCGA COAD-READ Project)

Hello, The TCGA project was done exclusively on humans. Please let me know if this does not answer

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Help with: Sample processing (TCGA COAD-READ Project)

Hello, The TCGA project was done exclusively on humans. Please let me know if this does not answer

May 13

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

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