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Figure 6 Combinations of multiple states of complexes. (A) Omitted notation in the EGFR Pathway Map. The 85 kDa regulatory subunit of phosphatidylinositol 3-kinase (PI3K (p85)) binds to active ErbB3 receptor via its phosphorylated tyrosine residues: Tyr1035, Tyr1178, Tyr1203/05, Tyr1241, Tyr1257, and Tyr1270. (B) Detailed portrayal of panel A for distinguishing the complexes according to differences of phosphotyrosine residues. ErbB3, erythroblastic leukemia viral (v-erb-b) oncogene homolog 3; PI3K (p85), 85 kDa regulatory subunit of phosphatidylinositol 3-kinase.

Figure 6 Combinations of multiple states of complexes. (A) Omitted notation in the EGFR Pathway Map. The 85 kDa regulatory subunit of phosphatidylinositol 3-kinase (PI3K (p85)) binds to active ErbB3 receptor via its phosphorylated tyrosine residues: Tyr1035, Tyr1178, Tyr1203/05, Tyr1241, Tyr1257, and Tyr1270. (B) Detailed portrayal of panel A for distinguishing the complexes according to differences of phosphotyrosine residues. ErbB3, erythroblastic leukemia viral (v-erb-b) oncogene homolog 3; PI3K (p85), 85 kDa regulatory subunit of phosphatidylinositol 3-kinase.

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Figure 2 The bow-tie architecture of the EGFR signaling pathway. A simplified diagram was created based on the EGFR signaling map in Figure 1. Arrows in this figure represent an informal notation of ‘flow of rea Various ligands bind to diverse receptor heterodimers, which then converge into a handful of molecules building a conserved core. Activities of these molecules play important roles in controlling diverse responses. Ni interactions are color-coded: red, positive feedback loop; blue, negative feedback loop; purple, inhibitory feed-forward path; green, crosstalk from GPCR cascade to EGFR cascade via calcium release. This image i available as high resolution PDF (see Supplementary PDF 2) or Scalable Vector Graphic (SVG).
Figure 2 The bow-tie architecture of the EGFR signaling pathway. A simplified diagram was created based on the EGFR signaling map in Figure 1. Arrows in this figure represent an informal notation of ‘flow of rea Various ligands bind to diverse receptor heterodimers, which then converge into a handful of molecules building a conserved core. Activities of these molecules play important roles in controlling diverse responses. Ni interactions are color-coded: red, positive feedback loop; blue, negative feedback loop; purple, inhibitory feed-forward path; green, crosstalk from GPCR cascade to EGFR cascade via calcium release. This image i available as high resolution PDF (see Supplementary PDF 2) or Scalable Vector Graphic (SVG).
Figure 3 Main symbols adopted by CellDesigner ver. 2.1.1. These symbols are provided in CellDesigner ver. 2.1.1. Size and color of each module are configurable. CellDesigner also provides X-Y coordinates for each module and can distinguish between cellular compartments. In this map, we employed a naming convention in which the localization of protein is indicated by a prefix to the protein name, such as ‘cyt.XX’ and ‘pl.m.XX’ for protein XX in the cytosol and protein XX at the plasma membrane, respectively. In addition, in order to provide a better overview and to understand pathways at a glance, we assigned unique names with an ‘address’ to a protein to express differences of combination states
Figure 3 Main symbols adopted by CellDesigner ver. 2.1.1. These symbols are provided in CellDesigner ver. 2.1.1. Size and color of each module are configurable. CellDesigner also provides X-Y coordinates for each module and can distinguish between cellular compartments. In this map, we employed a naming convention in which the localization of protein is indicated by a prefix to the protein name, such as ‘cyt.XX’ and ‘pl.m.XX’ for protein XX in the cytosol and protein XX at the plasma membrane, respectively. In addition, in order to provide a better overview and to understand pathways at a glance, we assigned unique names with an ‘address’ to a protein to express differences of combination states
Figure 4 Expression of the inner structures and states. The active state of the molecule is indicated by a dashed line surrounding the molecule. State changes of a component such as phosphorylation, acetylation, ubiquitination, and allosteric changes can be represented with specific information such as target residue and position.
Figure 4 Expression of the inner structures and states. The active state of the molecule is indicated by a dashed line surrounding the molecule. State changes of a component such as phosphorylation, acetylation, ubiquitination, and allosteric changes can be represented with specific information such as target residue and position.
shows the detailed scheme of combination states between EGFR and adaptors, while Figure 5B expresses combination states by assigning an ‘address’ to the name of a protein. The method of referring to proteins with an ‘address’ becomes clear using Grb2 as an example. Grb2 is recruited to the activated EGFR via the of protein species. For instance, Figure 5 provides the reader with a small part of the pathways illustrated in the map, namely interactions between EGFR and the three adaptor proteins, Src homology 2 domain containing transforming protein (Shc), Grb2, and GRB2-associated binding protein 1 (Gab1). Figure 5A
shows the detailed scheme of combination states between EGFR and adaptors, while Figure 5B expresses combination states by assigning an ‘address’ to the name of a protein. The method of referring to proteins with an ‘address’ becomes clear using Grb2 as an example. Grb2 is recruited to the activated EGFR via the of protein species. For instance, Figure 5 provides the reader with a small part of the pathways illustrated in the map, namely interactions between EGFR and the three adaptor proteins, Src homology 2 domain containing transforming protein (Shc), Grb2, and GRB2-associated binding protein 1 (Gab1). Figure 5A
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