Identification of core T cell network based on immunome interactome

BMC Systems Biology

Mauno Vihinen¹  Csaba Ortutay¹  Gabriel N Teku² 

[1] BioMediTech, University of Tampere, Tampere, Finland;Department of Experimental Medical Science, Lund University, Lund, Sweden

关键词: PPI;    Signaling;    TPPIN;    T cell;    Filtering;    Network;    Protein-protein interaction;   

Others  :  1141451
DOI  :  10.1186/1752-0509-8-17

 received in 2013-07-05, accepted in 2014-02-05,  发布年份 2014

【 摘 要 】

Background

Data-driven studies on the dynamics of reconstructed protein-protein interaction (PPI) networks facilitate investigation and identification of proteins important for particular processes or diseases and reduces time and costs of experimental verification. Modeling the dynamics of very large PPI networks is computationally costly.

Results

To circumvent this problem, we created a link-weighted human immunome interactome and performed filtering. We reconstructed the immunome interactome and weighed the links using jackknife gene expression correlation of integrated, time course gene expression data. Statistical significance of the links was computed using the Global Statistical Significance (GloSS) filtering algorithm. P-values from GloSS were computed for the integrated, time course gene expression data. We filtered the immunome interactome to identify core components of the T cell PPI network (TPPIN). The interconnectedness of the major pathways for T cell survival and response, including the T cell receptor, MAPK and JAK-STAT pathways, are maintained in the TPPIN network. The obtained TPPIN network is supported both by Gene Ontology term enrichment analysis along with study of essential genes enrichment.

Conclusions

By integrating gene expression data to the immunome interactome and using a weighted network filtering method, we identified the T cell PPI immune response network. This network reveals the most central and crucial network in T cells. The approach is general and applicable to any dataset that contains sufficient information.

【 授权许可】

   
2014 Teku et al.; licensee BioMed Central Ltd.

【 图 表 】

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