Thanks for sharing this great resource!

#ImmunoSky #Immunology

Please note that this summary is not doing justice to this excellent paper--I am merely sharing what I manage to read in a 30-minute reading session.

I highly recommend reading the paper for more cool tricks/ideas on using publicly available data to test your hypotheses.

The authors showed that the 42-gene SoM scores was, to some extent, correlated with Tsang's lab 150-gene Immune Health Metric (IHM) (Fig. S5).

Considering that IHM was derived using monogenic immune disorders, the authors proposed that the IHM reflects genetic factors while SoM lifestyle factors.

Using publicly available single-cell data, the authors showed that the scores were associated with certain immune cell types (Figs. 2D-E).

Detrimental scores were associated with neutrophils, protective scores with T/NK cells and monocytes.

SoM scores, or specifically its protective module scores, were associated with favourable response to hydrocortisone in burn injury patients (Figs. 1F-G)

How's the SoM score calculated in the first place?

SoM score = detrimental - protective scores.
Each of the detrimental/protective score was computed as the sum of scores of a few gene modules.
In turn, the gene modules were scored by taking the geometric mean of their respective genes.

The SoM score was identified using dataset of individuals with respiratory viral infections. By computing the score in bacterial infection datasets, the authors showed that the score was correlated with severe infection, irrespective of bacterial/viral etiology.

The score has numerous applications!

Thanks for taking the time to write the steps!

Oooh, how was the syncing? Do you have to manually export your annotations back to your computer?

Yes, in my experience, most figures are unreadable when printed in B/W :(

Oh I've been wrong many times, but the overwhelming majority was in private.

Absolutely not. But I think that is a skill that can only be acquired through such experience.

I have a naive question. What is the limit of data object size that can be tracked?

The community taught most of what I know and I feel compelled to give back. But when a senior researcher responded with a snarking remark, I could not help but feel terrible. A year has passed and I want to start anew on this platform. Does anyone have tips to handle such a situation?