Unequal evolutionary conservation of human protein interactions in interologous networks

Abstract

Background: Protein-protein interaction (PPI) networks have been transferred between organisms using interologs, allowing model organisms to supplement the interactomes of higher eukaryotes. However, the conservation of various network components has not been fully explored. Unequal conservation of certain network components may limit the ability to fully expand the target interactomes using interologs.

Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer

“…(ii) Annotation and enrichment analysis using 25 KEGG signaling pathways and cellular processes (Table S4C). (iii) Matching of differentially expressed genes to PPIs in I2D v1.72 (14,15) with additional PPI updates. Experimental PPI networks were generated by querying I2D with the target genes/proteins to obtain their immediate interacting proteins.…”

“…Although the number of overlapped genes was small, GO analysis still showed that these genes were enriched in genes of the extracellular region (9/14, P = 0.006) and KEGG pathways, including ECM-receptor interaction (3/14, P = 0.005) and focal adhesion (3/14, P = 0.01), which was in agreement with findings in the CAF vs. NF and tumor stroma vs. normal lung. Ten of the 14 genes were also mapped to protein-protein interactions (PPIs) in Interolog Interaction Database (I2D) v1.72 (14,15). Nine of the 10 genes/proteins interact via shared neighboring proteins (Fig.…”

A Survey on Evolutionary Analysis in PPI Networks

“…The authors concluded that obligate complexes are likely to co-evolve with their interacting partners, while transient interactions with an increased evolutionary rate show only little evidence for a correlated evolution of the interacting interfaces. This observation was later corroborated by Brown & Jurisica (2007) who analysed the presence of protein interactions across multiple species via orthology mapping and found that the greater the conservation of a protein interaction is, the higher the enrichment for stable complexes. Finally, Zinman et al (2011) extracted protein modules from a yeast integrated protein interaction network using various source of PPI evidence, and showed that interactions within modules were much more likely to be conserved than interactions between proteins in different modules.…”

Scalable, Integrative Analysis and Visualization of Protein Interactions

“…For example, the yeast interactome comprises 23,918 interactions according to DIP and 152,877 known and predicted interactions in I2D, the Interologous Interaction Database (http://ophid.utoronto.ca/i2d), an integrated database of PPIs from curated databases, experimental sources and predicted interactions (Niu et al, 2010;Brown and Jurisica, 2007;Brown and Jurisica 2005). While the researcher may only be interested in a small portion of the network in question, the scalability of an individual application and its analysis methods to networks of such size can be a considerable advantage.…”

“…One way of enriching our isolated data is by viewing it in the context of known and predicted interactions. I2D, the Interologous Interaction Database (http://ophid.utoronto.ca/i2d; (Brown et al, 2005, Brown et al, 2007), will be our source for these interactions. NAViGaTOR offers an I2D plug-in, which enables the researcher to easily add interactions to the existing graph.…”