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MaayanLab / sigcom-lincs

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Availability of the data matrix for UMAP analysis #63

Closed shkao closed 1 year ago

shkao commented 1 year ago

Hi,

I'm looking for certain genes in the interactive plotly UMAP. For example, I would like to know where TP53 is located in PC3-specific CRISPR Knockout Signatures.

I'm trying to hover over the whole plot and check the label, which is not very efficient for me. Would it be possible to provide the results of the UMAP, so that we can quickly locate the gene and its neighbors, for example:

UMAP-1, UMAP-2, Gene, Cluster
8, 9, INTS4, 13
11, 6, GPRC6A, 8

image

Also, at the top right corner of the UMAP page it says:

Signature queries: 4621
Gene queries: 754

However, by analyzing LINCS L1000 CRISPR Perturbations (2021) downloaded from SigCom, in celline PC3, I found 10,641 signatures from 5,096 genes. What would be the potential reasons for this inconsistency? (Signature queries: 4,621 vs 10,641; Gene queries: 754 vs 5,096)

u8sand commented 1 year ago

With respect to question about the metadata, this is a reasonable request, we will see what we can do about providing this metadata perhaps as an additional download on the portal.

With respect to the counts, it's " queries" because it has to do with the user submissions to the web portal and not with the actual number of signatures and genes, so these numbers are not expected to match.

shkao commented 1 year ago

Hi @u8sand ,

Thanks! Would you know what are the raw values for the UMAP analysis? Log2 fold changes or characteristic direction coefficients?

u8sand commented 1 year ago

@shkao This UMAP was made using the LINCS L1000 CRISPR Perturbations (2021) (https://maayanlab.cloud/sigcom-lincs/#/Download) file, which is characteristic direction coefficients.

Attached is the file you requested, we plan on adding it to the downloads soon. xpr_expanded.tsv.gz