Construction and analyses of human large-scale tissue specific networks

PLoS One. 2014 Dec 16;9(12):e115074. doi: 10.1371/journal.pone.0115074. eCollection 2014.

Abstract

Construction and analyses of tissue specific networks is crucial to unveil the function and organizational structure of biological systems. As a direct method to detect protein dynamics, human proteome-wide expression data provide an valuable resource to investigate the tissue specificity of proteins and interactions. By integrating protein expression data with large-scale interaction network, we constructed 30 tissue/cell specific networks in human and analyzed their properties and functions. Rather than the tissue specificity of proteins, we mainly focused on the tissue specificity of interactions to distill tissue specific networks. Through comparing our tissue specific networks with those inferred from gene expression data, we found our networks have larger scales and higher reliability. Furthermore, we investigated the similar extent of multiple tissue specific networks, which proved that tissues with similar functions tend to contain more common interactions. Finally, we found that the tissue specific networks differed from the static network in multiple topological properties. The proteins in tissue specific networks are interacting looser and the hubs play more important roles than those in the static network.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • Humans
  • Organ Specificity / genetics*
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps / genetics*
  • Proteome / genetics*
  • Proteomics
  • RNA, Messenger / genetics
  • Transcriptome / genetics*

Substances

  • Proteome
  • RNA, Messenger

Grants and funding

This work was supported by International Cooperation Project (2014DFB30010) and Chinese National Key Program of Basic Research (31171266). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.