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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;

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xiNET displays CLMS data in the context of other sequence information. Domains, or other annotated regions, are shown as color-coded segments of the bars or as color-coded sectors of the circles representing proteins. The start and end angles of a sector correspond to the start and end residues of the domain (residue 1 is at 12 o'clock). The data is a subset of the data from Herzog et al. (2). A live example containing the whole dataset can be seen at http://crosslinkviewer.org/figure8.html.
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Figure 8: xiNET displays CLMS data in the context of other sequence information. Domains, or other annotated regions, are shown as color-coded segments of the bars or as color-coded sectors of the circles representing proteins. The start and end angles of a sector correspond to the start and end residues of the domain (residue 1 is at 12 o'clock). The data is a subset of the data from Herzog et al. (2). A live example containing the whole dataset can be seen at http://crosslinkviewer.org/figure8.html.

Mentions: Fig. 8 illustrates a further aspect of xiNETs representation of sequence features such a domains. (Interactive figure at http://crosslinkviewer.org/figure8.html.) When proteins are shown as numbered bars, the domains are marked as colored regions along this bar. When the nodes are collapsed into a circle, domain annotation information is shown on these circular nodes as sectors, the start and end angles of which correspond to the start and end residues of the domain. Because the sectors are color-coded on the basis of their domain name, homologous proteins can be recognized by similar patterns in their colored sectors.


xiNET: cross-link network maps with residue resolution.

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

xiNET displays CLMS data in the context of other sequence information. Domains, or other annotated regions, are shown as color-coded segments of the bars or as color-coded sectors of the circles representing proteins. The start and end angles of a sector correspond to the start and end residues of the domain (residue 1 is at 12 o'clock). The data is a subset of the data from Herzog et al. (2). A live example containing the whole dataset can be seen at http://crosslinkviewer.org/figure8.html.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: xiNET displays CLMS data in the context of other sequence information. Domains, or other annotated regions, are shown as color-coded segments of the bars or as color-coded sectors of the circles representing proteins. The start and end angles of a sector correspond to the start and end residues of the domain (residue 1 is at 12 o'clock). The data is a subset of the data from Herzog et al. (2). A live example containing the whole dataset can be seen at http://crosslinkviewer.org/figure8.html.
Mentions: Fig. 8 illustrates a further aspect of xiNETs representation of sequence features such a domains. (Interactive figure at http://crosslinkviewer.org/figure8.html.) When proteins are shown as numbered bars, the domains are marked as colored regions along this bar. When the nodes are collapsed into a circle, domain annotation information is shown on these circular nodes as sectors, the start and end angles of which correspond to the start and end residues of the domain. Because the sectors are color-coded on the basis of their domain name, homologous proteins can be recognized by similar patterns in their colored sectors.

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