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BioMed Research International
Volume 2014, Article ID 397145, 12 pages
Research Article

The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions

Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 15701 Athens, Greece

Received 14 February 2014; Accepted 4 June 2014; Published 25 June 2014

Academic Editor: Tatsuya Akutsu

Copyright © 2014 Katerina C. Nastou et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

In Supplementary File 1, Figure S1 shows a sub-network of the sigma 1 subunit of the adaptor related protein AP2S1, a bottleneck protein of the network. Figure S2 illustrates a four layered network and is an example of the connections between a disease (Alzheimer’s) and the drugs associated with it, the peripheral proteins of the human plasma membrane interacting with these drugs and the interactions of these proteins. Figure S3 demonstrates two examples of complexes with novel components identified through the MCL clustering process. Figures S4, S5 and S6 display three Venn diagrams showing the overlap of GO terms for the Biological Process, Cellular Component and Molecular Function between the 238 peripheral membrane proteins and the 2374 proteins of the network.

In Supplementary File 2, Table S1 describes the dataset of 277 peripheral membrane proteins of the human plasma membrane. Table S2 contains the interactions for 238 peripheral membrane proteins as collected from IMEx and Table S3 includes only high-quality interactions as obtained from IntAct. Table S4 has information regarding the subcellular location of all the network’s proteins. Table S5 has extended information about proteins in the network with membrane binding domains and proteins located in lipid rafts. Tables S6 and S7 contain information about the drug association analysis. Table S8 describes the results from the MCL clustering process. Tables S9 and S10 describe the results from the GO term enrichment analysis. Table S11 provides information about essential proteins in the network. Table S12 holds information about the top ten hubs and bottlenecks in the network. Table S13 has an analysis of the characteristic path length of the network after the removal of certain or random nodes. Table S14 includes a comparison of proteins' subcellular locations for the IMEx and the IntAct networks. Table S15 has information about the function of all transmembrane proteins in the network. Table S16 has the subcellular location analysis for hubs and bottlenecks in the network. Table S17 includes a Fisher's Test for Drug categories associated with peripheral proteins of the human plasma membrane and Table S18 contains the disease enrichment analysis for peripheral membrane proteins using the human genome as a reference set for the analysis.

  1. Supplementary Material