Search results for query: NEGR1

...on chromosome 1:73,847,802 (chr1:73382119 on GRCh38 coordinates). DecodeME also seems to have a signal there, which we thought might point to NEGR1. I suspect the similarity is based on this: As DecodeME pointed to similar neural processes. Suspect it might also explain why chronic...

NEGR1 was at the 10th most significant locus and VRK2 was at the 25th most significant locus in DecodeME. The loci plots can be seen in this post...

...pathways. Single-nucleus RNA sequencing implicated excitatory neurons and astrocytes as key cellular contexts, emphasizing NCAM1–FGFR1 and NEGR1–NEGR1 signaling pathways. Mendelian randomization analyses provided causal evidence linking shared genetic liability to structural brain...

Oh right, my bad!

If it was specifically the PVN, I think it'd be more interesting. But it seems like what you quoted is an AI mentioning PVN linking to NEGR1 because it's the area of interest that was asked about, while in reality NEGR1 may be involved everywhere in the brain. And if the question was about any...

I think this is a really interesting connection to the PVN because the PVN apparantly mediates osmoregulation and so many pwME have issues with dehydration, excessive thirst, exessive and frequent urination (and sometimes in PEM the opposite - I need to drink loads but barely pee at all) etc. It...

I haven't really been able to follow what exactly you're doing. Maybe you could lay out your overarching plan, and maybe describe what everything in one row of the table on this webpage means?

By my calculation, NEGR1 is a bit closer: Lead variant of the locus is at: chr1:73,126,414 NEGR1: chr1:71,395,943-72,282,539 LRRIQ3: chr1:74,026,015-74,198,187 Distance to NEGR1: 73126414 - 72282539 = 843875 Distance to LRRIQ3: 74026015 - 73126414 = 899601 Though the difference is so small...

...need to request it, they say it’s free for academic use but it’s hit or miss if we count as academics!) But for now here’s the info I have for NEGR1 and for LRRIQ3 for comparison (both using GenomeBrowser database and a larger search window) It’s not ideal yet, it was only meant to be an...

On whether NEGR1 is actually the closest gene: The end of NEGR1 closest to the best hit is roughly at base pair 72,282,000 The best hit is roughly at base pair 73,200,000 The end of LRRIQ3 (another protein coding gene) is roughy at base pair 74,030,000. So, I think LRRIQ3 is closer. It's even...

I wonder how much of it comes from the bias that people used to look at/look for/study protein-coding genes and considered non-coding DNA "junk". I'm not saying he's wrong. I'm just wondering if and how the bias might be affecting current approaches and theories.

...is a lot more likely that relationships between enhancers and their nearest gene will be found. To flip to the other side, an argument why the NEGR1 gene could be relevant, looking at Forestglip's map: there are a lot of logp=3 significant hits in half of NEGR1 and it's a big gene, and so...

...DecodeME signal, making it less certain which genes are involved in ME/CFS. For genes like CA10 or DCC this is less of a problem. Agree that NEGR1 is not one of the strongest clues. On the other hand: none of the candidate genes has good certainty but we know pretty certain that some of...

Oh sorry, I did mischaracterize the quote I posted. I was thinking about this quote while writing that (which to be clear, seems like a somewhat reasonable idea to me):

To clarify: I didn't highlight NEGR1 much in my blog article because the gene was quite far from the DecodeME hit. I didn't assume ME/CFS is a nervous system disease and tried looking at potential genes from that angle. Instead, I focused on the protein-coding genes closest to DecodeME signals...

...would make sense. Whether we can be confident enough yet about (1) ME/CFS being primarily a neurological disease, or about (2) how well NEGR1's function would fit into that as opposed to other nearby genes, I'm not sure. I think other genetic evidence like DecodeME's MAGMA and the Zhang...

...at issue here: if we have a significant locus, and we have no other information, what's the likelihood that the nearest protein-coding gene (NEGR1 in this case) is the pathogenic gene implicated by the significant variant? A few months ago, there was a bit of discussion about this topic...

Yes, that’s what I was thinking and trying to dig into. I think I’ve noticed a problem in that my scripts look for all TFBS in a region rather than for a gene. This could explain the difference I was seeing and limit my results for enhancers away from the main gene, I’ll investigate and see if...

...of base pairs, so the area where there are good hits ( logp of around 7) are a really long way in base pair terms from the start of gene NEGR1. i.e 72,300,000 is approximately the start of NEGR1 and the good hits are 73,000,000 to 73.500,000. It's possible that the DecodeME Chromosome 1...

Yes. And no… I’m a bit confused on this tbh! If you look at the LocusZoom for NEGR1 you can see there’s a little arrow on the label for NEGR1pointing from right to left, that indicates it is read in that direction, so a promoter (that starts the read) would be off in that direction. And thst’s...