Secondly, using co-immunoprecipitation, a physical interaction of PTP1B with the membrane-associated IGF-1Rβ and higher phosphatase activity of the IGF-1Rβ-bound PTP1B fraction was observed further supporting our hypothesis and suggesting a key role of PTP1B in -driven repression of IGF-1 signalling.
One other type of edge, one that connects components but has no arrowhead, is used to depict a physical interaction between the components.
Here, we describe two methods that use FRET to detect a physical interaction between the T‐cell antigen receptor (TCR) and the CXCR4 chemokine receptor in living T lymphocytes.
While coimmunoprecipitation experiments could also have been used to test for a physical interaction between Corolla and Corona, these assays require a lot of starting material, and are not experimentally feasible for a protein interaction that happens in such a small number of cells.
For this predicted protein pair, we experimentally demonstrated a physical interaction, using three different set-ups.
Therefore, we investigated whether the dependence of ER α nuclear translocation on ERR β in the presence of oestrogen was based on a physical interaction using CoIP assays.
In these interactomes, each vertex represents a gene and each edge a physical interaction weighted using the product of the gene pair's percentile-normalized gene expression scores (Additional file 8: Figure S4).
For each pathway pair identified, we calculated the completeness scores d1, d2, d12 as defined in Equation (1) using the physical interaction data to measure the enrichment of physical interactions within pathway 1, within pathway 2, and between pathway 1 and pathway 2, respectively.
However, the pathways we identified do not necessarily adhere to this meaning; rather, functionally distinct genes may be found to be compensatory to a multifunction pathway since we did not use the physical interaction data.
As shown in Figure 5 bottom panel (boxes), these pathways showed enhanced functional homogeneity compared to Figure 5 upper panel (although still lower than that identified using physical interaction support; Figure 5, bottom panel, stars and circles).
