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Weird gene names in L1000 Consensus Signatures Coefficient Tables (Level 5) #77

Closed songsong0425 closed 10 months ago

songsong0425 commented 10 months ago

Dear MaayanLab members,

Greetings, always thank you for offering the valuable public dataset. I have a simple question about the data in the L1000 Consensus Signatures Coefficient Tables (Level 5).

When I downloaded CRISPR KO Consensus Signatures in the L1000 Consensus Signatures Coefficient Tables (Level 5) section, I found that there were some uncommon gene names in the dataset. Interestingly, the z-score of those genes is significant. Can anyone check what those genes are? I have attached the example cases. (first column: knock-outed gene, second column: perturbed gene, third column: z-score) image

I'm looking forward to hearing back from you. Thanks!

P.S. Do you have any plan for adding LINCS L1000 Overexpression Perturbations data in the L1000 Consensus Signatures Coefficient Tables (Level 5) section? If so, please let me know. Thank you.

sxie04 commented 10 months ago

Hi @songsong0425, the BRDN IDs come from the original L1000 profiles downloaded from the Broad Institute's CLUE.io resource. They likely refer to different plasmids targeting specific genes for knockout, but we do not currently have access to a mapping for the corresponding gene symbols. You may choose to filter these signatures out if you wish, as most of them probably targeted known genes already in the CRISPR KO data.

songsong0425 commented 10 months ago

Thank you for your reply! I removed the genes with BRDN ID from the dataset. Have a nice day!