importing gene signature scores into cBioportal

[Jinfeng Liu]

What's the best way of importing gene signature scores (e.g., IFNg signature scores calculated by ssGSEA or gsva) into cbioportal? It'd be great if we can do that and examine the correlation between gene signature scores and other measurements (e.g. mutation status and single-gene expression values).

thanks

Jinfeng

[Sjoerd van Hagen]

Hi Jinfeng,

How to load gene signature scores is described here: https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#gene-set-data

Have you already managed to set up cBioPortal locally?

Best,

Sjoerd.

--

E.   sjo...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl

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[bayes.gene]

Thanks Sjoerd. I have a related question regarding p-value for signature scores. As current GSVA doesn't generate p-value anymore, can I use some random p-values to fill in when preparing for the signature data?

Regards,

Biao

On Tuesday, August 4, 2020 at 3:00:44 AM UTC-7, Sjoerd van Hagen wrote:

Hi Jinfeng,

How to load gene signature scores is described here: https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#gene-set-data

Have you already managed to set up cBioPortal locally?

Best,

Sjoerd.

--

E.   sjo...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl

On Tue, Aug 4, 2020 at 5:36 AM Jinfeng Liu <jinfe...@gmail.com> wrote:

What's the best way of importing gene signature scores (e.g., IFNg signature scores calculated by ssGSEA or gsva) into cbioportal? It'd be great if we can do that and examine the correlation between gene signature scores and other measurements (e.g. mutation status and single-gene expression values).

thanks

Jinfeng

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[Sjoerd van Hagen]

Hi Biao,

Yes, you can assign all the samples the same p-value. I think you should still be able to use the old strategy for computing the p-values. If I remember correctly, it is just a matter of rerunning the algorithm with perturbed input to see how stable it is with respect to small changes.

Best,

Sjoerd.

--

E.   sjo...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl

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[Biao Li]

Thanks Sjoerd for the explanation.

Appreciate.

Biao

> On Aug 10, 2020, at 2:43 AM, Sjoerd van Hagen <sjo...@thehyve.nl> wrote:
>
> Hi Biao,
>
> Yes, you can assign all the samples the same p-value. I think you should still be able to use the old strategy for computing the p-values. If I remember correctly, it is just a matter of rerunning the algorithm with perturbed input to see how stable it is with respect to small changes.
>
> Best,
>
> Sjoerd.
>
>
> --
>
>
>

> E. sjo...@thehyve.nl
>
> T. +31(0)30 700 9713
>
> W. www.thehyve.nl
>
>
>
> On Sat, Aug 8, 2020 at 12:36 AM bayes.gene <bayes...@gmail.com> wrote:
> Thanks Sjoerd. I have a related question regarding p-value for signature scores. As current GSVA doesn't generate p-value anymore, can I use some random p-values to fill in when preparing for the signature data?
>
> Regards,
> Biao
>
> On Tuesday, August 4, 2020 at 3:00:44 AM UTC-7, Sjoerd van Hagen wrote:
> Hi Jinfeng,
>
> How to load gene signature scores is described here: https://github.com/cBioPortal/cbioportal/blob/master/docs/File-Formats.md#gene-set-data
>
> Have you already managed to set up cBioPortal locally?
>
> Best,
>
> Sjoerd.
> --
>
>
>

[Sjoerd van Hagen]

You're welcome.

Good luck!

--

E.   sjo...@thehyve.nl

T.   +31(0)30 700 9713

W.  www.thehyve.nl