Notes about all the analysis on Koichi DNA methylation data and other datasets
View the Project on GitHub AlexisHucteau/Koichi_Methylation_analysis
Analysis of DNA methylation through IDHm inhibitor treatment
Git des analyses de methylation de l’ADN en fonction du traitement à l’inhibiteur d’IDHm.
L’idée est de faire 5 groupes :
Et de discriminer les mutations IDH1 et IDH2
Comparer Bon et Mauvais responder at Baseline -> DMR_Response
Comparer Baseline et CD34+ -> DMR IDH
Prendre DMR specific de la réponse
Comparer Bon et Mauvais responder at post treatment -> DMR residuel
Comparer Post et Baseline -> DMR traitement
Prendre (DMR residuel - DMR traitement) union avec response specific DMR
Comparer ces response specific DMR avec les IDH specific DMR des WGBS.
| Pheno A | Pheno B | Number of DMRs | Number of genes | R object |
|---|---|---|---|---|
| Bad responder Baseline | Control CD34+ | 131 | 119 | DMR_Bad_Baseline_vs_Control_annotated |
| Good responder Baseline | Control CD34+ | 197 | 127 | DMR_Good_Baseline_vs_Control_annotated |
| Bad responder Baseline | Good responder Baseline | 240 | 321 | DMR_Good_vs_Bad_Baseline_annotated |
| Good Baseline vs Control | Bad Baseline vs Control | 62 | 94 | Specific_Bad_response_annotated |
| Bad responder Post treatment | Control CD34+ | 235 | 185 | DMR_Bad_Post_vs_Control_annotated |
| Good responder Post treatment | Control CD34+ | 109 | 68 | DMR_Good_Post_vs_Control_annotated |
| Good Post vs Control | Bad Post vs Control | 95 | 112 | Specific_Bad_response_post_annotated |
DMR IDH1 vs other AML subtypes
4388 DMRs
DMR IDH2 vs other AML subtypes
2552 DMRs
| DMR analysis | number of overlap with IDH1 | number of overlap with IDH2 | parameter changed of overlap | number of overlap with IDH1 | number of overlap with IDH2 |
|---|---|---|---|---|---|
| IDH1/2_DMR_WGBS_Good_responder_Baseline | 4 | 2 | max gap = 100 | 5 | 3 |
| IDH1/2_DMR_WGBS_Bad_responder_Baseline | 5 | 2 | max gap = 100 | 5 | 3 |
| IDH1/2_DMR_WGBS_Specific_Bad_responder_Baseline | 0 | 0 | max gap = 100 | 1 | 1 |
| IDH1/2_DMR_WGBS_Good_responder_Post | 2 | 1 | |||
| IDH1/2_DMR_WGBS_Bad_responder_Post | 2 | 0 | |||
| IDH1/2_DMR_WGBS_Specific_Bad_responder_Post | 0 | 0 |
| DMR analysis | Number of genes overlapping IDH1 | IDH2 | list of genes IDH1 | IDH2 |
|---|---|---|---|---|
| DMR_Good_Baseline_vs_Control_annotated | ||||
| DMR_Bad_Baseline_vs_Control_annotated | ||||
| Specific_Bad_response_annotated | ||||
| DMR_Bad_Post_vs_Control_annotated | ||||
| DMR_Good_Post_vs_Control_annotated | ||||
| Specific_Bad_response_post_annotated |