Alexis Hucteau PhD project
Notes about all the project advances and researches during the PhD
28.03.2022 - 01.04.2022 Week 13
28.03.2022
Looking at aracn effect on msviper TF activity prediction
Testing DeMAND-algorithm for Interrogating Drug Mechanism of Action using Network Dysregulation analysis
Using DeMAND, Mechanism of Action dyregulated NR vs R:
| moaGene | Pvalue | FDR |
|---|---|---|
| NOS2 | 1.517842e-11 | 4.551391e-08 |
| CYP17A1 | 2.937329e-11 | 4.551391e-08 |
| BIRC3 | 3.851648e-09 | 3.978752e-06 |
| IL2 | 8.886857e-08 | 6.885092e-05 |
| SELE | 2.475087e-07 | 1.534059e-04 |
| BCL2L1 | 9.864902e-07 | 4.485631e-04 |
Kullback-Leibler (KL) divergence:
| gene1 | gene2 | KLD | KLD.p |
|---|---|---|---|
| DLGAP1 | SOX2 | 9.08160044288928 | 0.001842360444131 |
| MYC | WDR36 | 8.27935400426403 | 0.002225292942782 |
| MYC | SFMBT1 | 8.27767843611966 | 0.002226212776101 |
| CYP17A1 | NFIC | 8.0767423217575 | 0.00234076542414 |
| PRF1 | STAT3 | 8.04440062134892 | 0.002360021079851 |
| JUN | NOS2 | 8.03554034015082 | 0.002365337512273 |
| NOS2 | RELA | 7.59128947444795 | 0.002656597252669 |
| FOS | NOS2 | 7.4782755495627 | 0.0027392172276 |
About NOS2: “Up-Regulation of iNOS in AML Blasts Creates an Immunosuppressive Microenvironment, Inhibits T-Cell Proliferation and Transforms T-Cells Towards a Tumor-Tolerating Phenotype”
In myeloid cells, the NF-κB complexes that bind to the nos2 promoter are p65/p65 and p50/p50 homodimers
29.03.2022
Downloading TCGA methylomes Running the RNAseq pipeline on PTBP1 data
30.03.2022
Trying to make a pchic network of genes of interest. Idea: Instead of 1 pchic w/ genes/tfs of interest + DMP/DMR -> 1 pchic w/ genes/tf of interest -> 1 pchic w/ DMR/DMP