Team-SB2

Meet-EU Team SB2 - Link to MEET-EU website

Topic B : Chromosome compartments

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Chromosome compartments project

Project of the MEET-U course for our university Sorbonne Université

Meetings : One meeting each week every wednesday afternoon from 4pm to 6pm

Responsability list :

Role	Name
Manager Expert	Rouquaya Mouss
Technician Expert	Damien Legros & Cédric Cornede
Scientific Expert	Hamid Hachemi
Delivrable Expert	Arnaud Quelin

Install and launch

First you need to clone our repository :

git clone https://github.com/meet-eu-21/Team-SB2

After that you have to install the requirements :

pip install -r requirements.txt

Then to launch the code :

python main.py

The following panel will come up, you can enter the numbers of the chromosomes you want to analyse and select the cell lines and the resolution (be careful ! : launching too many chromosomes can make a runtime memory error).

Here you have an example of the selection to run an analysis for GM12878, HUVEC and IMR90 with the chromosomes 11, X and 4 in 100kb.

The notebook Plot_histo.pynb can then be used to make the histograms of the results to compare the cell lines.

Our work

Class diagram of our code :

Our results for 100kb are available in the folder /Results

All .py files except color_b.py are used for our analysis. Two methods are used :

• With the first method, we search the number of compartments with an HMM using the data from the correlation matrix
• With the second method, we search the number of compartments with an HMM using the data from epigenetic marks.

The file color_b.py can be used with Pymol to see the colors of the compartments of the .pdb files of our results. (color_b.py can be put in Pymol folder, no need of the path before color_b.py in the following command if that's the case). You need to run the following commands in Pymol after opening the .pdb result you want to see :

run path_to_our_folder\Team-SB2\color_b.py
color_b()

Here is an example of the colors that can be seen on the .pdb file of chromosome 22 of HMEC with the compartments of the HMM method with correlation matrix :

Example of results

Example of data obtained with the correlation matrix method of chromosome 16 from GM12878 :

Example of data obtained with the epigenetic marks method of chromosome 16 from GM12878 :

Our predictions :

###################################HMM Contact###################################
Similarity score with Leopold: 74.972 %
Best compartment number : 7

###################################HMM Epigenetic###################################
Similarity score with Leopold: 64.673 %
Best compartment number : 5

HMM score with the correlation matrix method :

HMM score with epigenetic marks method :

Example of the histogram of results for HUVEC cell line :

For the correlation matrix method :

For the epigenetic method :