Questions about TCGA Provisional vs. PanCancer Atlas

[Oba,Junna]

Hello,

 

I would like to ask questions about mRNA expression TCGA data, Provisional vs. PanCancer Atlas.

 

When I click PanCancer Atlas for a study, in the “Select Patient/Case Set” panel and look for “tumors with mRNA data”, we tend to see the mRNA data from H133 microarray (green highlight), and when I click Provisional for a study, we tend to see mRNA-seq (V2) data. Some of provisional studies have not only RNA-seq V2 but also Agilent microarray and/or H133 microarray set. Some cancer types didn't have options to select “Tumors with mRNA data, for example, for Kidney Renal Papillary Cell Carcinoma (both Provisional and PanCancer Atlas).

Also, comparing the number of sample for each cancer type, there are some discrepancies between Provisional vs. PanCancer Atlas.

 

My questions are:

1) Are Provisional vs. PanCancer Atlas coming from the same or overlapping samples?

2) In general, TCGA Provisional has RNA-seq, and TCGA PanCancer Atlas microarray mRNA expression data? If so, were these analyses done separately?

3) For RNA-seq data, can we look at the actual RSEM or FPKM levels, and not the z-score?

 

I have pasted below what I have seen, as well as attached the excel spreadsheet to compare the sample number for each cancer type between Provisional vs. PanCancer Atlas.

I would really appreciate your answers and suggestions.

 

Thank you,

 

Junna Oba, MD, PhD

JO...@mdanderson.org

 

 

 

----------------------------------------------------------------------------------------------------------------------------------------------------------------

Abbreviation	Study Name	cBioPortal PanCancer	cBioPortal provisional	Note
ACC	Adrenocortical Carcinoma	78	79
BLCA	Bladder Urothelial Carcinoma	407	408
BRCA	Breast Invasive Carcinoma	1081	1100	provisional has also mRNA data from n=529 for Agilent microarray
CESC	Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma	293	306
CHOL	Cholangiocarcinoma	36	36
COAD	Colon Adenocarcinoma	276	NA	Colorectal adenocarcinoma, COREAD, provisional: 222 for Agilent microarray, 382 for RNA seq V2)
ESCA	Esophageal Carcinoma	181	185
GBM	Glioblastoma Multiforme	160	166	provisional has also mRNA data from n=401 for Agilent microarray and n=528 for U133 microarray
HNSC	Head and Neck Squamous Cell Carcinoma	515	522	provisional has also mRNA data from n=72 for Agilent microarray
KICH	Kidney Chromophobe	65	66
KIRC	Kidney Renal Clear Cell Carcinoma	510	534
KIRP	Kidney Renal Papillary Cell Carcinoma	NA	NA
LGG	Brain Lower Grade Glioma	514	530	provisional has also mRNA data from n=27 for Agilent microarray
LIHC	Liver Hepatocellular Carcinoma	366	373
LUAD	Lung Adenocarcinoma	510	517	provisional has also mRNA data from n=32 for Agilent microarray
LUSC	Lung Squamous Cell Carcinoma	484	NA
MESO	Mesothelioma	87	87
OV	Ovarian serous Cystadenocarcinoma	299	307	provisional has also mRNA data from n=558 for Agilent microarray and n=535 for U133 microarray
PAAD	Pancreatic Adenocarcinoma	177	179
PCPG	Pheochromocytoma and Paraganglioma	NA	184
PRAD	Prostate Adenocarcinoma	493	498
READ	Rectum Adenocarcinoma	89	NA	Colorectal adenocarcinoma, COREAD, provisional: 222 for Agilent microarray, 382 for RNA seq V2)
SARC	Sarcoma	NA	NA
SKCM	Skin Cutaneous Melanoma	443	472
STAD	Stomach Adenocarcinoma	401	415	provisional has also mRNA data from n=36 for RNA-seq (not V2)
TGCT	Testicular Germ Cell Cancer	NA	NA
THCA	Thyroid Carcinoma	NA	NA
THYM	Thymoma	119	120
UCEC	Uterine Corpus Endometrial Carcinoma	173	177	provisional has also mRNA data from n=54 for Agilent microarray
UCS	Uterine Carcinosarcoma	57	57
UVM	Uveal Melanoma	80	80
	Tumor Samples with mRNA data (U133 microarry only)
	Tumor Samples with mRNA data (RNA seq V2)

 

 

 

Breast Invasive Carcinoma (TCGA, Provisional) has “Tumor Samples with mRNA data (Agilent microarray) (529)” and “Tumor Samples with mRNA data (RNA-seq V2) (1100)”

 

Glioblastoma Multiforme (TCGA, Provisional) has “Tumor Samples with mRNA data (Agilent microarray) (401)”, “Tumor Samples with mRNA data (RNA-seq V2) (166)”, and “Tumor Samples with mRNA data (U133 microarray) (528)”.

 

Uveal Melanoma (TCGA, PanCnacer Atlas) has “Tumor Samples with mRNA data (U133 microarray only) (80)”, and

 

Uveal Melanoma (TCGA, Provisional) has “Tumor Samples with mRNA data (RNA-seq V2) (80)”

 

Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional) (TCGA, PanCancer Atlas), in both setting, did not have “Select Patient/Case Set” panel to choose “tumors with mRNA data”.

 

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[Kelsey Zhu]

Hi Junna, 

Provisional and PanCancer Atlas share some samples. Analyses were done separately. 

For RNA-seq data, you can look at the actual RSEM level by clicking on "Plots" tab on query result view, and then select "mRNA Expression (RNA Seq V2 RSEM)" from the Profile Name dropdown box(please see attached).

Best!

kelsey

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[JJ Gao]

Hi Junna,

Thank you for contacting us and providing the detailed comparison between pancan and provisional.

Provisional and Pancan expression data have a very large overlap in terms of samples and data itself. The provisional datasets in cBioPortal were retrieved from Firehose run of January 28, 2016 (https://gdac.broadinstitute.org/). The Pancan study were compiled for the Pancan analysis publised in cell (https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html). Their underlying data and samples were from the same TCGA source but data processing might be different.

The Pancan data has both microarray data and RNAseq v2 data while the Provisional data may miss one or both in certain cancer types. We recommend using the pancan data for TCGA data analysis.

You can use the DOWNLOAD DATA query form to download the RSEM data. You can also use Plots tab to look at the original data as Kelsey has pointed out.

I hope this is helpful. Please feel free to contact us for additional questions.

Best,

-JJ

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[Oba,Junna]

Hi JJ and Kelsey,

 

Thank you for your response and advice.

 

I am sorry if I am asking a silly question, but am I correct to understand that you suggest to go to the PanCancer data from GDC, in this page (https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html), and not cBioPortal itself, because currently cBioPortal does not show “RNA-seq V2” but “H133 microarray only” when I select “PanCancer Atlas”, then ““Select Patient/Case Set”?

 

For example, Uveal Melanoma (TCGA, PanCnacer Atlas) has “Tumor Samples with mRNA data (U133 microarray only) (80)”. And it is the case for all the other cancer types when I select “TCGA, PanCancer Atlas”.

 

 

Thank you very much for your help and support.

 

Sincerely,

 

Junna Oba

 

Glioblastoma Multiforme (TCGA, Provisional) has “Tumor Samples with mRNA data (Agilent microarray) (401)”, “Tumor Samples with mRNA data (RNA-seq V2) (166)”, and “Tumor Samples with mRNA data (U133 microarray) (528)”.

 

Uveal Melanoma (TCGA, PanCnacer Atlas) has “Tumor Samples with mRNA data (U133 microarray only) (80)”, and

 

Uveal Melanoma (TCGA, Provisional) has “Tumor Samples with mRNA data (RNA-seq V2) (80)”

 

Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional) (TCGA, PanCancer Atlas), in both setting, did not have “Select Patient/Case Set” panel to choose “tumors with mRNA data”.

 

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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[JJ Gao]

Hi Junna,

For TCGA PanCancer studies, you can select "All tumors" when querying. There is a bug that keeps us from generating the proper case list for RNASeq v2 data (we will fix that soon). But you can query the data by selecting the RNASeqV2 genetic profile in the "Select Genome Profile" section.

Thanks,

-JJ

[JJ Gao]

You are very welcome. Thanks for contacting us and using cBioPortal. -jj

On Mon, Jul 30, 2018 at 11:18 AM Oba,Junna <JO...@mdanderson.org> wrote:
>
> Hi JJ,
>
>
>
> Thank you for your quick response and answer.
>
> This has cleared my question, and I understand now.
>
>
>
> Thank you again for your help and support.

>
>
>
> Sincerely,
>
>
>
> Junna Oba
>
>
>
> From: JJ Gao [mailto:jianji...@gmail.com]
> Sent: Monday, July 30, 2018 9:57 AM
> To: Oba,Junna <JO...@mdanderson.org>
> Cc: Kelsey Zhu <kelse...@gmail.com>; cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
> Subject: Re: [cbioportal] Questions about TCGA Provisional vs. PanCancer Atlas
>
>
>
> Hi Junna,
>
>
>

> For TCGA PanCancer studies, you can select "All tumors" when querying. There is a bug that keeps us from generating the proper case list for RNASeq v2 data (we will fix that soon). But you can query the data by selecting the RNASeqV2 genetic profile in the "Select Genome Profile" section.
>
>
>
> Thanks,
>
> -JJ
>
>
>
> On Mon, Jul 30, 2018 at 12:24 AM Oba,Junna <JO...@mdanderson.org> wrote:
>
> Hi JJ and Kelsey,
>
>
>
> Thank you for your response and advice.
>
>
>
> I am sorry if I am asking a silly question, but am I correct to understand that you suggest to go to the PanCancer data from GDC, in this page (https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html), and not cBioPortal itself, because currently cBioPortal does not show “RNA-seq V2” but “H133 microarray only” when I select “PanCancer Atlas”, then ““Select Patient/Case Set”?
>
>
>
> For example, Uveal Melanoma (TCGA, PanCnacer Atlas) has “Tumor Samples with mRNA data (U133 microarray only) (80)”. And it is the case for all the other cancer types when I select “TCGA, PanCancer Atlas”.
>
>
>
>
>

> Thank you very much for your help and support.
>
>
>
> Sincerely,
>
>
>
> Junna Oba
>
>
>
>
>
>
>
> From: JJ Gao <jianji...@gmail.com>
> Date: Sunday, July 29, 2018 at 11:52 AM
> To: "Oba,Junna" <JO...@mdanderson.org>
> Cc: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>, Kelsey Zhu <kelse...@gmail.com>
> Subject: Re: [cbioportal] Questions about TCGA Provisional vs. PanCancer Atlas
>
>
>
> Hi Junna,
>
>
>
> Thank you for contacting us and providing the detailed comparison between pancan and provisional.
>
>
>
> Provisional and Pancan expression data have a very large overlap in terms of samples and data itself. The provisional datasets in cBioPortal were retrieved from Firehose run of January 28, 2016 (https://gdac.broadinstitute.org/). The Pancan study were compiled for the Pancan analysis publised in cell (https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html). Their underlying data and samples were from the same TCGA source but data processing might be different.
>
>
>
> The Pancan data has both microarray data and RNAseq v2 data while the Provisional data may miss one or both in certain cancer types. We recommend using the pancan data for TCGA data analysis.
>
>
>
> You can use the DOWNLOAD DATA query form to download the RSEM data. You can also use Plots tab to look at the original data as Kelsey has pointed out.
>
>
>
>
>

> Glioblastoma Multiforme (TCGA, Provisional) has “Tumor Samples with mRNA data (Agilent microarray) (401)”, “Tumor Samples with mRNA data (RNA-seq V2) (166)”, and “Tumor Samples with mRNA data (U133 microarray) (528)”.
>
>
>

> Uveal Melanoma (TCGA, PanCnacer Atlas) has “Tumor Samples with mRNA data (U133 microarray only) (80)”, and
>
>
>

> Uveal Melanoma (TCGA, Provisional) has “Tumor Samples with mRNA data (RNA-seq V2) (80)”
>
>
>

> Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional) (TCGA, PanCancer Atlas), in both setting, did not have “Select Patient/Case Set” panel to choose “tumors with mRNA data”.
>
>
>

[Oba,Junna]

Hi JJ,

 

Thank you for your quick response and answer.

This has cleared my question, and I understand now.

 

Thank you again for your help and support.

 

Sincerely,

 

Junna Oba

 

I hope this is helpful. Please feel free to contact us for additional questions.

 

Best,

-JJ

 

 

Glioblastoma Multiforme (TCGA, Provisional) has “Tumor Samples with mRNA data (Agilent microarray) (401)”, “Tumor Samples with mRNA data (RNA-seq V2) (166)”, and “Tumor Samples with mRNA data (U133 microarray) (528)”.

 

Uveal Melanoma (TCGA, PanCnacer Atlas) has “Tumor Samples with mRNA data (U133 microarray only) (80)”, and

 

Uveal Melanoma (TCGA, Provisional) has “Tumor Samples with mRNA data (RNA-seq V2) (80)”

 

Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional) (TCGA, PanCancer Atlas), in both setting, did not have “Select Patient/Case Set” panel to choose “tumors with mRNA data”.

 

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.