how to define the altered group in the the enrichment analysis of mRNA

[zhaoj...@gmail.com]

the altered and unalter group are classified based on the mRNA or mutaion of query genes?

[Ethan Cerami]

Dear zhaoj...@gmail.com:

Not sure if anyone wrote back to you on this yet, but the altered v. unaltered is based on whatever you provide within your query.  So, for example, if you enter EGFR and select mutations only, we create two groups:  one where EGFR is mutated, and one where EGFR is not mutated.

Hope that helps.

Ethan

[zhaoj...@gmail.com]

Dear Ethan:

Thanks for you reply.

I enter EGFR and seleect mutation and mRNA expression. Then in Enrichment-mRNA, the  altered v. unaltered means "EGRF muation vs wild-type" or "mRNA upregulated vs down regulated"?

在 2017年9月5日星期二 UTC+8下午10:10:18，Ethan Cerami写道：

[zhaoj...@gmail.com]

Hi, Ethan:

Thanks for your reply!

I entered EGFR and select both mutation and mRNA expression. In the mRNA enrichments analysis, the  altered v. unaltered  means "EGFR mutation vs wild type" or  "EGFR mRNA upregulated or downregulated"?

在 2017年9月5日星期二 UTC+8下午10:10:18，Ethan Cerami写道：

Dear zhaoj...@gmail.com:

[Nikolaus Schultz]

Then enrichment analysis will compare the EGFR altered samples (as defined in your query, in this case mutations) to those without an alteration.

To compare samples with high EGFR expression to those with low expression, you would have to define EGFR high expression in your query.

Niki.

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[tom...@stcube.com]

Hi Niki,

I'm trying to do something similar; compare K-M survival curves with high and low expression of genes of interest.  I can't seem to define high or low in the query.  I can defined altered expression as +/- Z scores, but that's not very helpful, as it includes the high and the low outliers together.  Am I supposed to do Gene: Exp > 0.5 (or whatever threshold I want to use)?  I'm trying to replicate work someone who has left did, and am having no success.

Thanks,

Tom

[JJ Gao]

Hi Tom,

Yes, OQL, e.g. Gene: Exp > 0.5, will solve your issue.

-JJ

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[Tala Bakheet]

[Tala Bakheet]

Dear Ethan,

I am trying to do an Enrichment-mRNA analysis , the  altered vs. unaltered for  a list of 500 separate genes . Is there a way to download the data in a batch mode.

Thanks,

Tala

On Tuesday, 5 September 2017 17:10:18 UTC+3, Ethan Cerami wrote:

On Tuesday, 5 September 2017 17:10:18 UTC+3, Ethan Cerami wrote:

[Tala Bakheet]

Yes, a total of 500 genes of different cancer.

Sent from my iPhone

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