JOBIM_Network

Poster Presentation

Connect Methylomes and Transcriptomes

In IDH1m cells, the DNA is up methylated. By looking at CpGs we can look at the specific localization of thoses methylations. The impact of methylations on genes is knwown to have a down regulation of their transcription. By connecting transcriptomics and methylomics data, we can see the direct impact of methylation due to the mutation.

To connect the two type of data, we first have to analyze both separetly. Then we have to connect the specific CpGs found to genes that are closed to. That means, looking at 3D conformation of the chromatine.

STEP 1

Analyze of the transcriptomes

STEP 1.1

Data 1

RNAseq from HL60 cell lines, a promyeloblast cell line. Somes are WT, others are IDH1 mutated, others are WT but treated with 2HG (the direct result of reaction by IDH1m) and others are WT treated by Octyl (a small molecule involoved in the transport of HG into the cells)

DATA : Transcriptomes/DATA_Transcriptomes/DATA

Samplesheet : Transcriptomes/Samplesheet_Transcriptomes

Scripts : Transcriptomes/Scripts_Transcriptomes/Transcriptomic_Analyze.Rmd

Results : Transcriptomes/Results_Transcriptomes

Gene_Ontology : Transcriptomes/Results_Transcriptomes/Gene_Ontology_enrichment

STEP 1.2

The list of genes that are differently expressed is poor for some comparision. To extend thoses lists we have to find the genes that are linked functionnaly to them. Thanks to networks like Biogrid or Reactome, we expend the data.

Data 2

List of genes for each comparison (WT/Mut, WT/WT+HG, WT+HG/MUT, WT/WT+Octyl, WT+Octyl/WT+HG) and in each direction (up or down regulation)

DATA : Transcriptomes/DATA_Transcriptomes/Results_Transcriptomes/[Comparison]/Genes_values/

With logFC threshold = 1.5 and P-value = 0.1

• 4 genes WT vs MUT UP regulation

• 3 genes WT vs MUT DOWN regulation

• 14 genes WT vs WT + HG UP regulation

• 5 genes WT vs WT + HG DOWN regulation

• 11 genes WT + HG vs MUT UP regulation

• 21 genes WT + HG vs MUT DOWN regulation

• 18 genes WT vs WT + Octyl UP regulation

• 2 genes WT vs WT + Octyl DOWN regulation

With logFC threshold = 0.75 and P-value = 0.1

• 8 genes WT + HG vs WT + Octyl UP regulation
• 6 genes WT + HG vs WT + Octyl DOWN regulation

Data 3

Networks from Biogrid and Reactome

DATA :

• Genes_Expension/Networks/BIOGRID-ORGANISM-Homo_sapiens-3.5.185.tab3.txt
• Genes_Expension/Networks/FIsInGene_020720_with_annotations.tsv

Results : Genes_Expension/Networks_of_new_genes

• 313 genes WT vs MUT UP regulation

• 11 genes WT vs MUT DOWN regulation

• 4 genes WT vs WT + HG UP regulation

• 3 genes WT vs WT + HG DOWN regulation

• 255 genes WT + HG vs MUT UP regulation

• 45 genes WT + HG vs MUT DOWN regulation

• 278 genes WT vs WT + Octyl UP regulation

• 0 genes WT vs WT + Octyl DOWN regulation

With logFC threshold = 0.75 and P-value = 0.1

• 24 genes WT + HG vs WT + Octyl UP regulation
• 75 genes WT + HG vs WT + Octyl DOWN regulation

Genes Networks Visualization : Genes_Expension/Genes_Networks_Visualizations/Genes_Networks_Visualization.cys

Gene Ontology Visualization : Genes_Expension/Gene_Ontology/Visualizations/Gene_Ontology.cys

Gene Ontology Table : Genes_Expension/Gene_Ontology/Tables/

Scripts : Genes_Expension/Scripts_Expension/Expend_genes.Rmd

STEP 2

Analyze of the methylomes

The aim of this analyze is to list CpGs that are differently methylated between the two condition IDH1 WT and IDH1 mutated.

Data 4

DATA : Methylomes/DATA_Methylomes/DATA

Samplesheet : Methylomes/Samplesheet_Methylomes

Scripts : Methylomes/Scripts_Methylomes

Results : Methylomes/Results_Methylomes

STEP 3

Connect CpGs to 3D contact

Data 5

Network of chromatine physical contact.

DATA : Chromatine_network/DATA/pchic.RData

Data 6

Chromosoms coordinates for CpGs that are differentially methylated between WT and Mutant

DATA : Chromatine_network/DATA/CpGs_mapinfo.csv

Script : Chromatine_network/Script/Find_Overlap.Rmd

Results : Chromatine_network/Results/CpGs_chromatine_Network.csv

STEP 4

Connect CpGs_Chromatine Network with Transcriptional analyses

Data 7

List of genes that are specifically up or down regulated

DATA : Genes_Expension/Networks_of_new_genes

Data 8

Network of specific CpGs differentially up or down methylated and their physical interaction with chromatine

DATA : Chromatine_network/Results/CpGs_chromatine_Network.csv

Scripts : Final_Network/Scripts/Connect_network.Rmd

Results : Final_Network/Results/????