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digitalcytometry / ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
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Will the marker gene vary with different discovery datasets? #73

Closed LynnChan99 closed 11 months ago

LynnChan99 commented 1 year ago

In your published article supplementary, the top 10 marker genes of 69 cell states were given, so , will the marker gene vary with different discovery datasets? or it just be the marker gene under your pan-cancer frame?

BALuca commented 1 year ago

Hi,

The markers presented in the paper are the pan-carcinoma ones. You can explore the histology-specific ones on our website in the section Explore Cell States & Ecotypes -> Cell State Signatures.

LynnChan99 commented 1 year ago

The marker genes are belong to the supplementary of your Cell article, I noticed that they are not similiar to the genes presented in the heatmap.So, what's the difference? ---- Replied Message ---- | From | @.> | | Date | 08/25/2023 17:06 | | To | @.> | | Cc | LynnChan99 @.>, Author @.> | | Subject | Re: [digitalcytometry/ecotyper] Will the marker gene vary with different discovery datasets? (Issue #73) |

Hi,

The markers presented in the paper are the pan-carcinoma ones. You can explore the histology-specific ones on our website in the section Explore Cell States & Ecotypes -> Cell State Signatures.

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BALuca commented 1 year ago

Which markers, heatmap and supplementary table?

LynnChan99 commented 1 year ago

Ok, I see. In your supplementary, the top 10 genes are from the single-cell data, but what I noticed in the pheatmap in ecotyper websites before are from core genes in cibersortx. If I want to calculate the abundance by ssgsea (I have already get the abundance of each of them seperately by ecotyper, and I need to calculate some combination of the specific cell states) , which gene list should I use?

Thanks, sorry for asking so many questions.

Best regards, Chan.

在 2023-08-25 17:27:14，"BALuca" @.***> 写道：

Which markers, heatmap and supplementary table?

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BALuca commented 1 year ago

Hi Chan,

I would recommend the single-cell version, since it is more comprehensive. I hope it helps!

Bogdan

LynnChan99 commented 1 year ago

Thanks!It's very helpful of your advice.

Hope you have a good day! ---- Replied Message ---- | From | @.> | | Date | 08/25/2023 19:10 | | To | digitalcytometry/ecotyper @.> | | Cc | LynnChan99 @.>, Author @.> | | Subject | Re: [digitalcytometry/ecotyper] Will the marker gene vary with different discovery datasets? (Issue #73) |

Hi Chan,

I would recommend the single-cell version, since it is more comprehensive. I hope it helps!

Bogdan

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