POLRID, SPATA25 connected to many genes: exploration for MorphMap paper (ORF, but want to check CRISPR)

[AnneCarpenter]

This was found in #11 as strong (+/-) correlation in ORF but not (completely) strongly connected in the KG (knowledge graph):

POLRID, SPATA25 look alike and are anti-correlated to a cluster of CAMK2A, GJB2, ATG7, MGLL, CCL14, PNPLA4; the pair is also anti-correlated individually to EML1, PER1, SLC39A1.

[auranic]

Of note in case it can be useful: a network visualization of the CAMK2A/ATG7/MGLL cluster. All links are "unexplained" links strong in ORF similarity, the edge width reflects the ORF similarity, and the color reflects the level of "explainability" (grey is more explainable, black is less explainable)

[AnneCarpenter]

oooh, that's a very helpful graphic, thank you!

[AnneCarpenter]

Waiting for chromosome-arm-corrected CRISPR data from @zahrahanifehlou before proceeding (probably it will not change the results but we don't want to waste time in case it does!)

(we are also waiting for tools from @tjetkaARD to make heatmaps that include KG+ and KG- genes to provide more context when we are zooming into a cluster with some KG- connections in it.)

[niranjchandrasekaran]

Notebook

The heatmap shows the percentile of the cosine similarities (1 → similar, 0 → anti-similar). The text is the maximum of the absolute KG score (gene_mf__go, gene_bp_go, gene_pathway). I set a KG threshold (like we previously had) of 0.4. If connections have a score lesser than this threshold, then the connection is considered to be unknown. The KG scores were downloaded from Google Drive: ORF and CRISPR. The diagonal of the heatmap indicates whether a gene has a phenotype (False could also mean the gene is not present in the dataset).

POLRID does not have a phenotype in both ORF and CRISPR. SPATA25 is still highly anti-similar to several genes. Many of these connections are unknown.

ORF

CRISPR

[AnneCarpenter]

Niranj, for this kind of plot where we've done little followup work, it may be more valuable to (a) re-define the cluster of interest rather than (b) select the precise list of genes from the first version - there really wasn't anything special about them and it would be hard to explain why we included the set if they're largely based on the prior version of profiles.
Can you clarify which of these you did?

[niranjchandrasekaran]

I am hoping that the ones we have done followup work will be sufficient for the paper. But if they aren't, then I can look take the (a) route. For now, I have taken the (b) route.

[niranjchandrasekaran]

Since we have not done a lot of follow up on this story, I am putting it on hold. Will reopen if needed.