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UCSC Xena and Cancer Genomics Browser

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5/26/20

Xena paper just published!

We're excited to announce that our paper was just published in Nature Biotechnology! We hope that

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Xena paper just published!

We're excited to announce that our paper was just published in Nature Biotechnology! We hope that

5/26/20

IzThed, Mary Goldman3

Sep 1

Missing samples from: TCGA TARGET GTEx transcript expression by RSEM using UCSC TOIL RNA-seq recompute

Hello Mary, Great I will have a look, thanks for the fast reply. 😊 Best, Theo From: Mary Goldman <

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Missing samples from: TCGA TARGET GTEx transcript expression by RSEM using UCSC TOIL RNA-seq recompute

Hello Mary, Great I will have a look, thanks for the fast reply. 😊 Best, Theo From: Mary Goldman <

Sep 1

Christian Mazzeo, … Mary Goldman15

Aug 26

TCGA TARGET GTEx dataset

Hi Shen, Sorry, but we are not funded to advise about tools other than UCSC Xena. Personally I have

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TCGA TARGET GTEx dataset

Hi Shen, Sorry, but we are not funded to advise about tools other than UCSC Xena. Personally I have

Aug 26

周金, Mary Goldman2

Jul 7

Questions related to the GDC MP2PRT-ALL database

Hello, I believe they collected the initial sample from the patient before treatment and then

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Questions related to the GDC MP2PRT-ALL database

Hello, I believe they collected the initial sample from the patient before treatment and then

Jul 7

Krishna Sriram, Mary Goldman2

Jul 3

TCGA single cell data

Hi Krishna, Thanks for bringing this to our attention. This dataset was actually labeled incorrectly.

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TCGA single cell data

Hi Krishna, Thanks for bringing this to our attention. This dataset was actually labeled incorrectly.

Jul 3

Jammm Chung, Mary Goldman2

Jun 19

Missing RNA-seq Download Link for TCGA-READ Dataset on Xena

Hi Jammm, There are 4 RNAseq datasets for TCGA READ ( https://xenabrowser.net/datapages/?cohort=TCGA%

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Missing RNA-seq Download Link for TCGA-READ Dataset on Xena

Hi Jammm, There are 4 RNAseq datasets for TCGA READ ( https://xenabrowser.net/datapages/?cohort=TCGA%

Jun 19

Changjin Hong, Mary Goldman3

May 24

TRANSCRIPTS analysis is not available?

Hello, Transcript View is working now. Let us know if you see any issues. Best, Mary ----- Mary

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TRANSCRIPTS analysis is not available?

Hello, Transcript View is working now. Let us know if you see any issues. Best, Mary ----- Mary

May 24

Edie Lee, Mary Goldman2

May 15

How to remove certain type of sample from a dataset?

Hi Edie, The easiest way to do this is to sequentially remove samples with EGFR aberrations and then

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How to remove certain type of sample from a dataset?

Hi Edie, The easiest way to do this is to sequentially remove samples with EGFR aberrations and then

May 15

Cavina K Lee, Mary Goldman2

Feb 21

discrepancy in PAAD cohort

Hi Cavina, Can you give me a bit more information as to what you're seeing? As a first pass is

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discrepancy in PAAD cohort

Hi Cavina, Can you give me a bit more information as to what you're seeing? As a first pass is

Feb 21

山口裕美, Mary Goldman3

Jan 16

error of downloading a local Xena Hub

Hello, Thank you for your patience. You should now be able to download a local Xena hub. Please let

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error of downloading a local Xena Hub

Hello, Thank you for your patience. You should now be able to download a local Xena hub. Please let

Jan 16

Jiale Wu, Mary Goldman2

Jan 15

Gene isoform information of CCLE cell lines

Hi Jiale, Unfortunately this is not possible. The TRANSCRIPTS visualization only has data from the

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Gene isoform information of CCLE cell lines

Hi Jiale, Unfortunately this is not possible. The TRANSCRIPTS visualization only has data from the

Jan 15

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

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