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I used to like dancing and if I could again I would like that too. Is this a ‘nice things are nice’ paper?

My original post stuck to the practical and was more focused on what could be done than the difficulties and what cannot. Partly I suppose because that’s the way I like to share things that may be useful and partly because I assume all severe people know certain things. As so well communicated...

Thanks all, bought a couple of things to try and I will report back!

It didn’t load for me so I missed that treat!

Wasn’t sure where best to post this or how wide the interest would be so piggybacking on this thread. While looking at different tools and APIs I’ve increasingly found MCP servers being provided by organisations, for example: https://www.ebi.ac.uk/ols4/mcp https://string-db.org/help//mcp/ What...

Sonya even gave them the headline in “2025: A breakthrough year for ME, but we must go further” Good article making the argument for investment in research though.

They’re just clusters of genes with similar patterns of tissue expression. I haven’t dug into what their functions are yet. In each chart the bars on the left are the silhouette scores of every gene in every cluster, while the right hand side is the overall score for each cluster as a whole.

Basically yeah. A measure of how close a data point is to others in its cluster compared to those in other clusters. I discuss a bit and give some links in my posts here.

Here’s the silhouette analysis charts of each cluster around the peaks, some reasonable looking clusters which seem to be refined but also others which undergo quite a lot of fragmentation. Not sure what to make of this or where to try the enrichment steps to be most informative (maybe 5, 11 and...

Nice find @forestglip and what a story! This has reminded me to try throwing the top 115 genes at my scripts and see what comes up. And I need to reread the analysis you did. Here’s the silhouette metrics, a couple of peaks but also looks maybe quite fragmented, will need to dig in some more...

I’ve thought about them but have no idea how to choose one, any recommendations? Thanks, have found some decent looking Besox clippers. Quite fancy keeping my fingertips though! :)

Thanks @Trish I feel there could be a joke here about the text being in silhouette…

Thanks for digging in to this. Something seemed off but I wasn’t sure if it was me or the paper! Great to have an explanation.

Mainly silhouette, I also looked at SSE and the heat-maps visually. I've never heard of NbClust. Looks like an R package and I’m not at all familiar with R. Would be really interested to hear what you find using it though. (Btw, for some reason half of your message didn’t show up for me, looks...

I couldn’t find a way to automate creation of these and include in the report, so did it manually, but here’s each cluster of genes on string-db for people to experiment with if they wish. Clustering with k=5 PrecisionLife DecodeME data, k5 z, cluster 1 PrecisionLife DecodeME data, k5 z...

It would! OLFM4 isn’t even in the PrecisionLife gene list. Only CSE1L and DCC are in both I think. Not sure what to make of that or if it’s worth looking at a combined gene set to see what turns up…

Rather than starting another thread, this is one of the papers quoted, and one of many from the Pluznick Lab at Johns Hopkins, here’s a list of their publications in this area and a quote from their website Olfactory receptor responding to gut microbiota-derived signals plays a role in renin...

Those 3 also looks like they have the highest FDRs and visually are above 0.05 although I think they mention using that as the cutoff? Am I reading that right? Just wondering if it’s relevant, only recently started learning about false discovery rates!

Does anyone have any recommendations? I’m looking for good quality, easy to use and will last. Sometimes cutting and filing can be too much effort but when up to it, or if broken up over time, it’s a little bit of self csre which can be quite enjoyable. So worth getting some good tools and am...

Another read on olfactory receptors. This review paints a picture of wider implications in cardiovascular, inflammatory processes, kidney and metabolism. It also talks about the signalling pathways. Could have some clues to why even if not a causal factor these mechanisms could be affected and...