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eQTL Looking at gene expression datasets, there wasn't really a result that matched the DecodeME signal well (all PP.H4 < 0.8). Phewas Looking at genetic studies of other traits, gave almost no results - very different from other loci. Two reached a PP.H4 of 0.8 or higher, dementia in the...

3D contacts with Hi-C The domains that show how the region often folds and touches in 3D points also points to the western region where UNC13C lies, and none includes the genes to the east. More info and background about this analysis is given here. The link to UNC13C in the west is also seen...

Had a closer look at this locus. The top SNP is a bit of an outlier ( lower p-value and imputation score than the SNPs it is in near perfect correlation with). So I think the signal is slightly below the significance threshold, but that doesn't matter much. chromatin openess and histone marks...

Here's what this plot looks like, it did not replicate in the Nott et al. dataset of neurons. More info about the datasets and methodology I used here. The Hi-C data from 5 ENCODE brain samples show a different picture though. No special connection to NEGR1 but to ERICH3 and LRRC53. So...

Yes. I mainly tested the neuronal cells because of the MAGMA enrichment analysis in the brain but also because POU3F2 is mainly expressed there: Tissue expression of POU3F2 - Summary - The Human Protein Atlas

Yes, I plan to do these analyses (eqtl, phewas, AlphaGenome, chromatin openness, Hi-C) on all DecodeME hits with p < 10^-6. Most of the time these analyzes don't give much extra insight, but sometimes they help refine the predictions of the FLAMES algorithm for what the most plausible causal...

Chromatin conformation I've been looking more into databases on 3-D contact: based on how the chromatin is folded, locations that are far apart on the DNA string can actually be close. It is particularly useful when the GWAS signal is in a gene desert, far away from protein-coding genes. The...

Anyone has any insights on this one. My first thought is that it might be a big deal if LLM can improve itself by tinkering with the weights directly. Sparks of Weight-Space Programming: LLMs can natively read & write neural network weights

I think the high genetic correlations with fibromyalgia, irritable bowel syndrome and self-reported CFS (rg > 0.7) compared to a much lower correlation for measures of intelligence and education (rg < 0.2) suggest that the majority of the signal reflects the diseases and not participation bias.I...

Some more studies here https://s4me.info/threads/abnormalities-in-response-to-vasopressin-infusion-in-chronic-fatigue-syndrome-2001-altemus-et-al.48566/post-676043

1) We’ve written a new article about the spectacular progress in artificial intelligence (AI), the billions that AI companies are investing to transform drug discovery, and why this is a reason for hope for ME/CFS patients. https://mecfsscience.org/the-ai-revolution/ Here's a brief summary...

That's what I used. I suspect the results could come from one of the enhancers here such as EH38E3437846. It points to T-cell but the z-score didn't really stood out (< 3) in my analysis.

Thought this was an interesting aspect of NEGR1. It reminded me of ARFGEF2 bringing GABA-A receptors to the cell surface. Source: Neuronal growth regulator 1 (NEGR1) promotes synaptic targeting of glutamic acid decarboxylase 65 (GAD65) | bioRxiv

My analysis didn't reveal much in this region. The credible set was large with 385 SNPs. The eQTL didn't show any gene expression dataset with a similar signal (coloc PP.H4 > 0.8). The closest signal was a weak one for NEGR1 in the esophagus GTEx_v10 dataset (PP.H4 = 0.62, p-value 0.000039)...

The FLAMES algorithm predicted MMS22L for this region with high confidence. But I think it's because FLAMES is restricted to a 750 kb window (filter = 7500000 in this file) so it didn't consider other genes such as POU3F2. It probably only saw MMS22L in the 750 kb window and gave it a high score...

Distance is usually measured to the transcription start site (TSS) of a gene, the place where the reading starts. Both genes are read in the <- direction so they are read from right to left and the TSS is on the right side of the gene. For NEGR1 the TSS is 72,282,539 For LRRIQ3 the TSS is...

Some other relevant studies: Spacing and orientation of bipartite DNA-binding motifs as potential functional determinants for POU domain factors - PubMed A requirement for the POU transcription factor, Brn-2, in corticotropin-releasing hormone expression in a neuronal cell line - PubMed The...

This article doesn't have the best timing: Low-Dose Naltrexone Linked to Some Long COVID Improvements | MedPage Today

Anyone has the full text of this paper? Roles of POU3F2 in Brain Development and Neuropsychiatric Disorders Roles of POU3F2 in Brain Development and Neuropsychiatric Disorders - Liu - 2026 - Developmental Neurobiology - Wiley Online Library

The prioritzation of FBXL4 in the preprint seems to be mostly based on it being the closest gene. But it is not really close and the 3D chromatin data suggested a link with POU3F2 which is also the strongest brain-based protein coding gene nearby. So my guess for this locus is that it points to...