is it still possible to run enrichment analysis on all data?

Question

is it still possible to run enrichment analysis on all data?

Closed this issue 2 years ago · 5 comments

Hi team,
This tool is amazing and thanks for keeping it running and updating.
I was wondering if it is possible to run enrichment analysis on all experiment types, i.e. including histone ChIPseq, TF ChIPseq and ATACseq etc, as before?
Currently, there is no all option for the experiment type. I would like to have something like that, similar to all cell type in the cell type box.
Thank you if you are able to provide this.
Cheers,
Alex

Answer 1 · 2022-01-10T12:30:41.000Z

Hi Alex, Thank you for using ChIP-Atlas. The enrichment analysis with all experiment types is not available in recent version of ChIP-Atlas because the computation time becomes too longer. So, run the enrichment analysis with histone ChIPseq, TF ChIPseq and ATAC-seq etc, separately, and concatenate the resulted TSV files. Cheers, Shinya

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2022/01/10 20:48、Feng Yan ***@***.***>のメール: Hi team, This tool is amazing and thanks for keeping it running and updating. I was wondering if it is possible to run enrichment analysis on all experiment types, i.e. including histone ChIPseq, TF ChIPseq and ATACseq etc, as before? Currently, there is no all option for the experiment type. I would like to have something like that, similar to all cell type in the cell type box. Thank you if you are able to provide this. Cheers, Alex — Reply to this email directly, view it on GitHub <#56>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADD2CTNRK3BF22RUB4E5Y5TUVLBRZANCNFSM5LTONLUA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.

Answer 2 · 2022-01-25T00:09:14.000Z

Thank you, Shinya, for your suggestions.
Actually, I want to run my enrichment analysis against a few samples and data that are unclassified in your database, which I have manually checked and is related to my research. For example, those data:

SRX021808 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021809 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021810 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021811 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021812 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021813 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021814 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021815 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021816 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021817 | mm10 | Unclassified | Unclassified | Pluripotent stem cell
SRX021818 | mm10 | Unclassified | Unclassified | Pluripotent stem cell

Is there a way to make the results include them? That is why I prefer to have an ALL option for factors as well.
Cheers,
Alex

Answer 3 · 2022-01-25T00:33:56.000Z

Hi Alex, Thank you for you detailed explanation. Unfortunately, ChIP-Atlas Web service cannot perform enrichment analysis with ChIP-seq data whose antigens are unclassified. Instead, I can perform the analysis in my local computer if you can send me your query data (gene list or BED file) together with the settings you specified in the Web service. Shinya

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Answer 4 · 2022-01-25T00:45:15.000Z

That would be great! btw, how can I find your email? Or do I post links here?

Answer 5 · 2022-01-25T00:52:35.000Z

Send your data to oki.shinya.3w [at] kyoto-u.ac.jp <http://kyoto-u.ac.jp/>, directly.

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2022/01/25 9:45、Feng Yan ***@***.***>のメール: That would be great! btw, how can I find your email? Or do I post links here? — Reply to this email directly, view it on GitHub <#56 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADD2CTIX45TUVPTWS2QYY4TUXXXCXANCNFSM5LTONLUA>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.