Reporting initial result of data analysis

[swiri021]

[swiri021]

@kicheolkim It seems CIS and RR has DiseaseDuration difference significantly (notebook link), so if we find features that are relevant to early and late markers by using DiseaseDuration, those might be differential expressed genes between RR and CIS. Do you think CIS and RR have actual meaning for the early and late stages of MS? for example, CIS might be really the early stage of MS and RR for the medium stage.

[kicheolkim]

@swiri021 I don't think RR can consider as a middle of the stage. As far as I know, in clinics, CIS is just experienced the first time neurodegeneration. If the patient had an attack again, it considers as the RR stage. A patient can have more attacks or have no more attacks after the CIS stage. That's why I think the data is good for disease mechanisms study but may not be good for diagnostic biomarkers.

[swiri021]

• Compared AUCs of SVM models between DEG features and activation score features, and activation score model has higher AUC for same CD4 result.
• Notebooks :
  SVM with DEG features, SVM with activation score features

[kicheolkim]

wow... it's very interesting...
Is the state single gene? or gene set? Is there a list of the genes?

[swiri021]

wow... it's very interesting... Is the state single gene? or gene set? Is there a list of the genes?

Activation score is calculated by gene-sets(gene signatures), and DEG is one list of DEG as you know... So, here, DEG model is using one gene as one features and Activation Score model is using one pathway score as one feature.