2nd year plan and ideas

• In vitro replicates
• DNA methylation
• WGBS
• new k-mers cohort
• Starting a paper
• Test other TF activity methods
  • Aracn
• Look at other transcriptional datasets even if they are not IDH treatments
• Look at enrichment of monocytes granulocytes in the different datasets
• Gradient diff patients
• Dediff
• Stem cells and RAS pathways
• Look at other cancer

In vitro replicates

Rhod2, CD15, CD38, western blot (myc, nfkb, Bcl2)

DNA methylation

Combine DNA methylation on promoter to the tf network analysis

Combine DNA methylation on enhancer using chromatine conformation

WGBS

Finish analysing Whole Genome Bisulfite Sequencing

New k-mers cohort

Look at our patients cohort with k-mers.

Starting a paper

• AML
• IDH
• TF activity
• Network analysis
• DNA methylation
• In vitro experiments
• In vivo? experiments/perspectives chrom structure

Test other TF activity methods

i-cisTargets

Aracn

Look at and test Aracn

Look at other transcriptional datasets even if they are not IDH treatments

Same as new k-mers cohort

Look at enrichment of monocytes granulocytes in the different datasets

Differentiation may be linked to resistance. Look at diff enrichment and IDHm response. Look at cell lines too.

Gradient diff patients

Main idea as above.

Dédiff

Investigate on this process.

Stem cells and RAS pathways

Ras signaling linked to stemness

Look at other cancer

NF-kB SMAD3 found in melanoma