In silico prediction of protein-protein interactions in human macrophages

BMC Research Notes

Alia Benkahla¹  Christine Brun³  Slimane Ben Miled²  Fatma Guerfali¹  Oussema Souiai³ 

[1] LIVGM + Laboratory of Medical Parasitology, Biotechnology and Biomolecules, Institut Pasteur de Tunis, Avenue Jugurtha, Tunis, Tunisia;ENIT-LAMSIN BP 37, Tunis, Tunisia;TAGC, Inserm UMR_S 1090, Aix-Marseille Université, Marseille, France

关键词: Inference;    Macrophage;    Contextualisation;    Protein interaction network;   

Others  :  1134229
DOI  :  10.1186/1756-0500-7-157

 received in 2013-05-14, accepted in 2014-03-07,  发布年份 2014

【 摘 要 】

Background

Protein-protein interaction (PPI) network analyses are highly valuable in deciphering and understanding the intricate organisation of cellular functions. Nevertheless, the majority of available protein-protein interaction networks are context-less, i.e. without any reference to the spatial, temporal or physiological conditions in which the interactions may occur. In this work, we are proposing a protocol to infer the most likely protein-protein interaction (PPI) network in human macrophages.

Results

We integrated the PPI dataset from the Agile Protein Interaction DataAnalyzer (APID) with different meta-data to infer a contextualized macrophage-specific interactome using a combination of statistical methods. The obtained interactome is enriched in experimentally verified interactions and in proteins involved in macrophage-related biological processes (i.e. immune response activation, regulation of apoptosis). As a case study, we used the contextualized interactome to highlight the cellular processes induced upon Mycobacterium tuberculosis infection.

Conclusion

Our work confirms that contextualizing interactomes improves the biological significance of bioinformatic analyses. More specifically, studying such inferred network rather than focusing at the gene expression level only, is informative on the processes involved in the host response. Indeed, important immune features such as apoptosis are solely highlighted when the spotlight is on the protein interaction level.

【 授权许可】

   
2014 Souiai et al.; licensee BioMed Central Ltd.

【 图 表 】

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