Hello, I am new to depmap and i am finding it hard interpreting the data, specially the T-statistic value for genes and P values, what they imply? I am trying to look at essential genes in a cancer subtype. Can anyone here guide me or provide a link to any resource (i have found only one youtube vide and that dont answers my questions). Its an urgent and important call for help, i hope to hear back. thank you.
There’s many places that we report p-values and there’s several places where I can imagine we might be reporting t-statistics so I’m not sure which you’re referring to. How to interpret is really going to depend on the context in which these were computed.
Can you provide an example of where in the portal or the datasets which you are trying to interpret? (If it’s somewhere in the portal, screenshots are often the quickest way to describe what you’re looking at)
Thanks,
Phil
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Thank you so much for the response phil, i will try to make my question more clear here. I am trying to look at gene dependencies enriched in oral squamous cell carcinoma (OSCC), there are more than 3000 dependencies enriched in OSCC in depmap data, and i want to filter out the genes that were found to be more essential for majority of the cell lines. The data is given in T-statistics and i am finding it hard interpreting it. This reply box is not acccepting a screenshot so I am providing a link to what i am looking at below for more clarity.
https://depmap.org/portal/context/Oral%20Cavity%20Squamous%20Cell%20Carcinoma
I hope to hear back from you soon.
thanks,
Yussi
I have gone through some threads in the forum regarding T-statistics and P values and what i have understood is that the t-statistic is a difference in means of gene effect scores in the cell lines included in the “context” and all the rest of the cell lines that are not included. The P value is a value that tells us how significant the t-statistic is. Now, can we say the genes with lowest t-statistic ( negative values) are more essential for the cell lines in the context and does a positive T-statistic indicates that the knock down of the gene has been observed to be in favour of cell viability? I wonder why the data dont follow a sequence where genes with the top negative t-statistic values should have enrichment in the lineage and lower values should not have (it appears to follow a little, but then you have genes with lower t-statistics that are not mentioned to be enriched on the gene page and then genes with comparatively higher values wtih enrichment mentioned) when you open the gene page. A little guidance and a quicker response would be highly appreciated.
Thanks,
yussi
