How to preserve mouse specific genes when downloading it from get_library()

[Smilenone]

Hi, I am going to use KEGG_2019_Mouse to study mouse related pathways, where I used code:
KEGG_mouse = gp.get_library(name='KEGG_2019_Mouse', organism='mouse')
However, the downloaded genes are Human genes symbols, I had to to use bm.query() in your toturial to convert them to Mouse. In this process, 0~1096 genes in different pathways are dropped. Making a result that in each pathways, the converted version has less genes than the origin one. Does this a true result, or a bad phenomenon because of the ID convertion? Can I download the KEGG_2019_Mouse in the mouse gene symbols directly?

[zqfang]

You can download the gmt file directly from here: https://maayanlab.cloud/Enrichr/#libraries

Unfortunately, enrichr website use the same gmts for both human and mouse (all upcases)

[Smilenone]

Thanks for your timely response!

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------------------ 原始邮件 ------------------ 发件人: "zqfang/GSEApy" ***@***.***>; 发送时间: 2023年5月20日(星期六) 上午7:11 ***@***.***>; 抄送: "Qunlun ***@***.******@***.***>; 主题: Re: [zqfang/GSEApy] How to preserve mouse specific genes when downloading it from get_library() (Issue #204) You can download the gmt file directly from here: https://maayanlab.cloud/Enrichr/#libraries Unfortunately, enrichr website use the same gmts for both human and mouse (all upcases) — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[zqfang]

v1.0.6 now have the MSIGDB api to download mouse GMT file with gene symbol/entrezid directory. close now