Limits...
xiNET: cross-link network maps with residue resolution.

Combe CW, Fischer L, Rappsilber J - Mol. Cell Proteomics (2015)

Bottom Line: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results.The interactive maps of the cross-link network that it generates are a type of node-link diagram.In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. xiNET is open source, released under the Apache version 2 license.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;

Show MeSH

Related in: MedlinePlus

Six different node-link diagrams of the same CLMS data. The data is from Chen et al. (1), A, is an extract from that paper designed to show how the CLMS evidence supports the location of a dimerization domain between Tfg1 and Tfg2. B–F, show alternative node-link diagrams (of the interprotein links only) produced using D3 (20). B, shows the typical use of node-link diagrams in biology, where nodes represent whole molecules (line width has been used to represent the number of links). C, uses distinct nodes to represent the linked residues, as is typical of RIN tools such as RINalyzer (12). In the absence of other information to guide the layout, C, uses a force directed layout. D, attempts to bring some order to the layout by arranging the nodes around a circle. E, again uses a circular layout but this time the placement of the nodes on the perimeter is determined by the linked residue's position in the protein sequence. F, shows a HivePlot (16) of the data, in which the categories (axes) represent each of the three proteins and the distance along the axis is determined by residue position in the sequence. A, E and F succeed in making an association between the individual cross-links and domain-level features: B, C, and D do not. To make this association it is necessary to use the position of the linked residues within the overall protein sequence to guide the placement of the nodes.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4390258&req=5

Figure 1: Six different node-link diagrams of the same CLMS data. The data is from Chen et al. (1), A, is an extract from that paper designed to show how the CLMS evidence supports the location of a dimerization domain between Tfg1 and Tfg2. B–F, show alternative node-link diagrams (of the interprotein links only) produced using D3 (20). B, shows the typical use of node-link diagrams in biology, where nodes represent whole molecules (line width has been used to represent the number of links). C, uses distinct nodes to represent the linked residues, as is typical of RIN tools such as RINalyzer (12). In the absence of other information to guide the layout, C, uses a force directed layout. D, attempts to bring some order to the layout by arranging the nodes around a circle. E, again uses a circular layout but this time the placement of the nodes on the perimeter is determined by the linked residue's position in the protein sequence. F, shows a HivePlot (16) of the data, in which the categories (axes) represent each of the three proteins and the distance along the axis is determined by residue position in the sequence. A, E and F succeed in making an association between the individual cross-links and domain-level features: B, C, and D do not. To make this association it is necessary to use the position of the linked residues within the overall protein sequence to guide the placement of the nodes.

Mentions: This is illustrated in Fig. 1, which shows six node-link representations of the same CLMS data. For simplicity, we use only the inter-protein cross-links from this dataset, omitting self-links (links back to a protein of the same type). The data is taken from Chen et al. (1), who investigated the structure of the RNA polymerase II-TFIIF complex. Essential to their conclusions is CLMS evidence for the locations of dimerization domains between Tfg1 and Tgf2.


xiNET: cross-link network maps with residue resolution.

Combe CW, Fischer L, Rappsilber J - Mol. Cell Proteomics (2015)

Six different node-link diagrams of the same CLMS data. The data is from Chen et al. (1), A, is an extract from that paper designed to show how the CLMS evidence supports the location of a dimerization domain between Tfg1 and Tfg2. B–F, show alternative node-link diagrams (of the interprotein links only) produced using D3 (20). B, shows the typical use of node-link diagrams in biology, where nodes represent whole molecules (line width has been used to represent the number of links). C, uses distinct nodes to represent the linked residues, as is typical of RIN tools such as RINalyzer (12). In the absence of other information to guide the layout, C, uses a force directed layout. D, attempts to bring some order to the layout by arranging the nodes around a circle. E, again uses a circular layout but this time the placement of the nodes on the perimeter is determined by the linked residue's position in the protein sequence. F, shows a HivePlot (16) of the data, in which the categories (axes) represent each of the three proteins and the distance along the axis is determined by residue position in the sequence. A, E and F succeed in making an association between the individual cross-links and domain-level features: B, C, and D do not. To make this association it is necessary to use the position of the linked residues within the overall protein sequence to guide the placement of the nodes.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4390258&req=5

Figure 1: Six different node-link diagrams of the same CLMS data. The data is from Chen et al. (1), A, is an extract from that paper designed to show how the CLMS evidence supports the location of a dimerization domain between Tfg1 and Tfg2. B–F, show alternative node-link diagrams (of the interprotein links only) produced using D3 (20). B, shows the typical use of node-link diagrams in biology, where nodes represent whole molecules (line width has been used to represent the number of links). C, uses distinct nodes to represent the linked residues, as is typical of RIN tools such as RINalyzer (12). In the absence of other information to guide the layout, C, uses a force directed layout. D, attempts to bring some order to the layout by arranging the nodes around a circle. E, again uses a circular layout but this time the placement of the nodes on the perimeter is determined by the linked residue's position in the protein sequence. F, shows a HivePlot (16) of the data, in which the categories (axes) represent each of the three proteins and the distance along the axis is determined by residue position in the sequence. A, E and F succeed in making an association between the individual cross-links and domain-level features: B, C, and D do not. To make this association it is necessary to use the position of the linked residues within the overall protein sequence to guide the placement of the nodes.
Mentions: This is illustrated in Fig. 1, which shows six node-link representations of the same CLMS data. For simplicity, we use only the inter-protein cross-links from this dataset, omitting self-links (links back to a protein of the same type). The data is taken from Chen et al. (1), who investigated the structure of the RNA polymerase II-TFIIF complex. Essential to their conclusions is CLMS evidence for the locations of dimerization domains between Tfg1 and Tgf2.

Bottom Line: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results.The interactive maps of the cross-link network that it generates are a type of node-link diagram.In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. xiNET is open source, released under the Apache version 2 license.

View Article: PubMed Central - PubMed

Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;

Show MeSH
Related in: MedlinePlus