Personal project: Sick Genes, a website for compiling significant gene findings from studies on ME/CFS and other conditions

[wigglethemouse]

A lot of parts I wasn't sure about, like what differentially accessible here means:

I assume they are referring to differential chromatin accessible, where differential is either between PwME vs Control, or before and after CPET difference. From the paper:

Thus, we used ATAC-seq to compare chromatin accessibilities of TM (and TN) cells in the same cohort of patients and healthy controls profiled by RNA-seq, identifying 67,189 consensus chromatin-accessible regions (ChARs) across all conditions. Accessible regions were enriched at transcriptional start sites, as expected for reliable ATAC-seq profiles (SI Appendix, Fig. S4A).

That is a rather technical paper and I agree it's difficult to understand. Well done for trying.

According to AI in simple terms, chromatin accessibility refers to how "open" or "loose" the DNA is within a cell's nucleus. To understand this, it helps to know that our DNA isn't just a free-floating strand; it's tightly wound and packaged with proteins, primarily histones, into structures called chromatin.
Open vs. Closed Chromatin:

• Open (Accessible) Chromatin: Imagine a loosely wound spool of thread. In this state, the DNA is more exposed and available.
• Closed (Inaccessible) Chromatin: This is like a tightly wound, compact spool. The DNA is hidden and unavailable.

 

[forestglip]

I assume they are referring to chromatin accessible. From the paper:


According to AI in simple terms, chromatin accessibility refers to how "open" or "loose" the DNA is within a cell's nucleus. To understand this, it helps to know that our DNA isn't just a free-floating strand; it's tightly wound and packaged with proteins, primarily histones, into structures called chromatin.
Open vs. Closed Chromatin:

• Open (Accessible) Chromatin: Imagine a loosely wound spool of thread. In this state, the DNA is more exposed and available.
• Closed (Inaccessible) Chromatin: This is like a tightly wound, compact spool. The DNA is hidden and unavailable.

I see, thanks. So the DNA is a bit looser or denser near these genes in ME/CFS is I think what I'm getting. That's a type of finding I'd never seen before. But I think it makes sense to add along with mutations and abundance since it's a finding that is different from controls and refers to a change related to a specific gene.

 

[Turtle]

Edit: I think I'll post things when recording genes that aren't very straightforward on this thread like above, just in case anyone has any suggestions. But I think it's okay if it's not perfect. I might miss some genes or mistakenly mark some genes as significant based on a misunderstanding, but I don't think it's a big deal if the vast majority of genes recorded are correct. Just a bit of noise in the data.

Good insight!!
A bit of noise on paper, is OK.

 

[hotblack]

I suppose in those borderline cases it’s probably best to cast the net wider and have more in there than less? It can always be narrowed down later, when someone digs more into a paper/when experts are using it and provide feedback that a gene isn’t relevant/appropriate for inclusion.

 

[Amw66]

A lot of hard work , thank you @forestglip

 

[EndME]

How do you envision people using this database @forestglip? I was thinking, if I was a researcher that just completed a genetic study and found some statistically significant genes I would want to know how the previous literature would look like. Now your website will instantly be able to tell how often a my genes had been significant previously but it won't be able to tell me how often it was not significant which arguably might be just as important. I'm not sure how that could be handled without introducing even more work. What are your thoughts on this?