information about units of mRNAseqV2

[Polo Alessandro]

Dear cBioPortal staff,

I am Alessandro Polo and I am currently working on my master thesis at Centro di Riverimento Oncologico (CRO) in Aviano, Italy.

My thesis is partially based on gene expression (RNAseq) analysis of data from cBioPortal. However, it is somewhat unspecified which units are used on these data.

Specifically, I would like to know what is the exact unit of the Genomic Profile "mRNA expression (RNA Seq V2 RSEM)" data in the "Breast Invasive Carcinoma (TCGA, Provisional)" Study obtainable from the "Download" section of your website's home page. Are they expressed in TPMs or another RNAseq unit? Are they normalized through upper quartile and/or log2? 

Secondly, I understand RNAseq z-scores are based on RNAseqV2 RSEM data. Are z-scores calculated on TPMs too?

Thank you for your attention,

Alessandro Polo

[Nikolaus Schultz]

Hi Alessandro,

We use normalized RSEM counts as provided by the Broad Firehose, and we use those for z-scores as well. 

You can find more information about the RSEM method here:

http://seqanswers.com/forums/showthread.php?t=42911

Niki.

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[Nikolaus Schultz]

Yes, you can use the data to compare expression levels within a sample and between samples of the same study. If you want to compare expression levels across studies, you can only do this within TCGA studies. 

Niki.

On May 29, 2019, at 12:26 PM, Damiano Valentina <vdam...@cro.it> wrote:

Dear Nikolau,

thank you for your response.

We are wondering whether RNA Seq V2 RSEM data can be used to perform gene expression comparison within a sample and between different samples.

Thank you in advance.

Regards,

Valentina

Dr Valentina Damiano
Unit of Functional Onco-genomics and Genetics
Centro di Riferimento Oncologico di Aviano (CRO), IRCCS
33081 Aviano (PN)
Italy
Tel: +39 0434659590

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Da: Nikolaus Schultz [nsch...@gmail.com]
Inviato: martedì 21 maggio 2019 17.39
A: Polo Alessandro
Cc: cbiop...@googlegroups.com; Damiano Valentina
Oggetto: Re: [cbioportal] information about units of mRNAseqV2

[Damiano Valentina]

Dear Nikolau,

thank you for your response.

We are wondering whether RNA Seq V2 RSEM data can be used to perform gene expression comparison within a sample and between different samples.

Thank you in advance.

Regards,

Valentina

Dr Valentina Damiano
Unit of Functional Onco-genomics and Genetics
Centro di Riferimento Oncologico di Aviano (CRO), IRCCS
33081 Aviano (PN)
Italy
Tel: +39 0434659590

---

Da: Nikolaus Schultz [nsch...@gmail.com]
Inviato: martedì 21 maggio 2019 17.39
A: Polo Alessandro
Cc: cbiop...@googlegroups.com; Damiano Valentina
Oggetto: Re: [cbioportal] information about units of mRNAseqV2