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
Default key for xiNET figures. Any of the lines representing links may be dashed to indicate the link is ambiguous regarding linkage site. Note that self-links can be ambiguous regarding whether they are intra or intermolecular. The default key can be modified by users/developers to adapt it to their specific representation needs. Typically, such modifications involve assigning line color to an attribute of the cross-links, for example quantitation or confidence attributes.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4390258&req=5

Figure 3: Default key for xiNET figures. Any of the lines representing links may be dashed to indicate the link is ambiguous regarding linkage site. Note that self-links can be ambiguous regarding whether they are intra or intermolecular. The default key can be modified by users/developers to adapt it to their specific representation needs. Typically, such modifications involve assigning line color to an attribute of the cross-links, for example quantitation or confidence attributes.

Mentions: In this section, we provide detailed instructions for creating a xiNET map by uploading data to the website (Uploading Data to Website) or, to keep all data fully within the user's control, by using the tool locally (Local Use). We show these maps and then (Further Examples) briefly introduce other examples needed to illustrate all the features of xiNET. Fig. 3 shows the default legend for xiNET, which is used in the output shown.


xiNET: cross-link network maps with residue resolution.

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

Default key for xiNET figures. Any of the lines representing links may be dashed to indicate the link is ambiguous regarding linkage site. Note that self-links can be ambiguous regarding whether they are intra or intermolecular. The default key can be modified by users/developers to adapt it to their specific representation needs. Typically, such modifications involve assigning line color to an attribute of the cross-links, for example quantitation or confidence attributes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Default key for xiNET figures. Any of the lines representing links may be dashed to indicate the link is ambiguous regarding linkage site. Note that self-links can be ambiguous regarding whether they are intra or intermolecular. The default key can be modified by users/developers to adapt it to their specific representation needs. Typically, such modifications involve assigning line color to an attribute of the cross-links, for example quantitation or confidence attributes.
Mentions: In this section, we provide detailed instructions for creating a xiNET map by uploading data to the website (Uploading Data to Website) or, to keep all data fully within the user's control, by using the tool locally (Local Use). We show these maps and then (Further Examples) briefly introduce other examples needed to illustrate all the features of xiNET. Fig. 3 shows the default legend for xiNET, which is used in the output shown.

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