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BraneMF: Integration of Biological Networks for Functional Analysis of Proteins

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BraneMF: Integration of Biological Networks for Functional Analysis of Proteins

Citation

Surabhi Jagtap, Abdulkadir Çelikkanat, Aurélie Pirayre, Frédérique Bidard, Laurent Duval, Fragkiskos D Malliaros, BraneMF: integration of biological networks for functional analysis of proteins, Bioinformatics, Volume 38, Issue 24, 15 December 2022, Pages 5383–5389, https://doi.org/10.1093/bioinformatics/btac691

BraneMF

Create a virtual environment with conda

1. Create a virtual environment with name 'branemf'

conda create -n branemf python=3.6

2. Activate the virtual environment

conda activate branemf

3. Install the required packages

pip install -r requirements.txt

4. Download the precomputed PPMI matrix files

Google drive: https://drive.google.com/drive/folders/1X5Gj5udIPKiLEvzeKWuUucnWw5AZOsnY?usp=sharing 

To compute PPMI matrices from String networks, run the following command by providing taxanomy ID of the organism (e.g 4932: yeast, 9606: human) other organisms: https://stringdb-static.org/download/species.v11.5.txt

 python BraneMF_buildPPMI.py --O 4932

5. Computation of embeddings

run file: branemf.m 

To reproduce the results, use precomuted embeddings and following commands

6. Perform clustering and GO enrichment

python cluster_enrichment.py --emb ./data/emb/yeast_branemf_w1_alpha_1.emb --k 40 --sim 20 --genes ./data/yeast_string_genes.txt

7. Perform protein function prediction

python Protein_function_prediction.py --emb ./emb/Integrated_emb/BraneMF_emb_sel/w10/Org4932BraneMF_g1_d128_w10_23May2022.emb  --anno ./data/org_4932_BPl1.txt --trials 10

8. Perform protein Interaction prediction

a. Prepare the training and test sets.

python ppi_pre_preprocess_files.py --new ./data/yeast_string_refnet_2021.txt --old ./data/old_ppis.txt --genes ./data/yeast_string_genes.txt

b. compute the scores

python predict_ppi.py --emb ./data/emb/yeast_branemf_w3_alpha_1.emb --train ./data/train.pkl --test ./data/test.pkl

9. Perform Network reconstruction

python net_reconst.py --emb ./data/emb/yeast_branemf_w1_alpha_1.emb --refnet ./data/yeast_string_refnet_2021.txt --genes ./data/yeast_string_genes.txt

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