jrahimik / RA

Rheumatoid arthritis RA endotype, heritatbility estimation and ppi network assesment
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Writing the results Fig2 #4

Open jrahimik opened 1 year ago

jrahimik commented 1 year ago

-[] Describe Figure 2, I have to set up the question.(Not a report to say what I have done, just say why I have done it). -[p] literature gene finding

jrahimik commented 1 year ago

-[] Figure 2: Rheumatoid arthritis (RA) is a multifaceted autoimmune disorder characterized by a complex interplay of genetic factors and the disruption of various cellular and molecular processes. Two crucial diagnostic criteria for identifying RA are the presence of rheumatoid factor (RF) and anti-citrullinated peptide (CCP) antibodies in the bloodstream. However, it remains unclear whether the distinction between these two markers signifies mere variations in biological indicators or represents distinct subtypes of RA.(Difference in genetic basis of two groups because we suspect that there is genetic differences between these two groups), To explore this issue, we conducted an in-depth analysis involving approximately 900 RA patients. This cohort was divided into two halves: one group with concurrent positivity for CCP and RF (referred to as double positive - DP), and the other group with solely RF positivity (RF). Employing a meticulous approach based on restricted maximum likelihood, we computed the divergence in heritability between the DP and RF cohorts. [I will add details regrading the covariates and etc][Strikingly, a substantial difference in heritability (~30%) with standard deviation of (~16%) emerged between these groups, indicating fundamental distinctions in the inherent risk and underpinnings of these two endotypes of RA. Subsequently, a genome-wide association analysis (GWAS) was conducted, I will add details regrading the covariates and etc],[How benforroni correction and number of snps and also these number of snps doesn't account for the difference in the genetic difference] leading to the identification of SNP () the proximity HLA-DR5 and HLA-DRA locus as accounting for a portion, albeit not the entirety, of the observed contrast in heritability between DP and RF subtypes of RA as shown in (Fig .2b).

jrahimik commented 1 year ago

Here is the updated version:

https://docs.google.com/document/d/10omYwti1PAF38MpF-kjXCYW2KZNOeCh4Sh0Z1uuidBg/edit?usp=sharing

jrahimik commented 1 year ago

@jrahimik double check LD and talk more about snps @jrahimik check the standard deviation of overall portioned heritability