GlyConnect Compozitor 1.0.0

About

Compozitor queries the GlyConnect database to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarising information searched in the database.

Citation

Robin T, Mariethoz J, Lisacek F (2020)
Examining and fine-tuning the selection of glycan compositions with GlyConnect Compozitor, Mol Cell Proteomics

Composition

The following table summarises the basic constituents of glycan compositions:

Notation

GlyConnect notation

Uses the abbreviated code for residues (see table) and a semicolon as a separator between this code and the corresponding number of residues. Each such pair is separated from the next by a space. The N-glycan core is represented in this notation as: Hex:3 HexNAc:2.

Byonic notation

Uses the abbreviated code for residues and brackets to delineate the corresponding number of residues for this code. No space separates code-number pairs. The N-glycan core is represented in this notation as: Hex(3)HexNAc(2).

Condensed notation

Uses the condensed code (see table) immediately followed by the corresponding number of residues. No space separates code-number pairs. The N-glycan core is represented as: h2N2.

Functionalities

The range of user actions in the interface is illustrated in this library of GIFs:

Data input

Node information

Path information

Graph handling

Glycan property barplot

Graph information

Virtual nodes

These nodes are computed by performing the systematic pairwise comparison of all compositions in a graph. If two compositions differ from exactly two residues, the two corresponding nodes are tentatively connected through an intermediary node that is only one residue away from each. Then, this tentative node is added only if it meets two conditions:

1. It does not already exist in the graph
2. None of its children has a non-virtual parent node.

The second rule avoids overcrowding the graph with multiple alternative paths. The introduction of virtual nodes increases the connectivity of a graph.

Node size

reflects the number of recorded publications supporting the corresponding composition

Node label

• The inner label reflects the number of solved structures stored in the database for the corresponding composition.
• The inner label reflects the number of solved structures stored in the database for the corresponding composition.

Node colour

Reflects the results of up to three queries launched successively:

• A single query result is named A and displayed in a graph with blue nodes.
• A double query results are named A and B and displayed respectively in blue (A) and red (B).
• A triple query results are named A, B and C and displayed respectively in blue (A) and red (B) and green (C).
• Shared compositions between several sets of results are shown in magenta (common to A and B), yellow (common to A and C), cyan (common to B and C) and black (common to all).

Path label

The letter of the condensed notation, corresponding to the added residue.

Path colours

Reflect the action of the user:

• Positioning the cursor on a node highlights entering paths in cyan and exiting paths in orange.
• Positioning the cursor on a path label highlights all paths sharing this label according to the following:

Selection

Format

Compositions

Selection

Format

Compositions