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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Useyma Gülhan, Mary Goldman2

12/9/24

LTBP1 Gene expression and KM Plot

Hi Useyma, While I do verify that the graphs you created are accurate given the underlying data, we

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LTBP1 Gene expression and KM Plot

Hi Useyma, While I do verify that the graphs you created are accurate given the underlying data, we

12/9/24

Lin lingo, Mary Goldman2

11/21/24

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

11/21/24

Ghislain Breton, Mary Goldman2

11/14/24

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,

11/14/24

CR F, Mary Goldman2

11/6/24

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

11/6/24

Donogh O'Brien, Mary Goldman4

10/29/24

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

10/29/24

Marissa D, Mary Goldman2

10/23/24

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

10/23/24

Jacob Neumann, Mary Goldman2

10/23/24

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

10/23/24

Enrique Medina-Acosta, Mary Goldman2

10/16/24

[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

10/16/24

Alex Azizi, Mary Goldman3

10/8/24

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

10/8/24

初子斌, Mary Goldman2

9/3/24

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

9/3/24

8/21/24

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

8/21/24

Özge Yüksel, Mary Goldman2

7/18/24

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.

7/18/24

Zhicheng Zhou, Mary Goldman2

7/15/24

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

7/15/24

Joan Frigola Rissech, Mary Goldman2

7/1/24

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.

7/1/24

Arpita Mohapatra, Mary Goldman2

6/26/24

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

6/26/24

Arpita Mohapatra, Mary Goldman2

6/24/24

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

6/24/24

Karen Vara, Mary Goldman2

5/13/24

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

5/13/24

Sandhya, Mary Goldman2

4/11/24

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

4/11/24

Racha Hosni, … Mary Goldman4

4/8/24

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

4/8/24

Karen Vara, Mary Goldman2

4/3/24

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

4/3/24

Racha Hosni, Mary Goldman2

3/27/24

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

3/27/24

Federico Nichetti, Mary Goldman2

2/20/24

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

2/20/24

Vladimir Wischnewski, Mary Goldman3

2/13/24

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

2/13/24

Karen Vara, … Mary Goldman4

2/12/24

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

2/12/24

Ashwin Mukund, … Mary Goldman4

2/9/24

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

2/9/24

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

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