- CVCL_VU59 15B
- CVCL_VT75 17cl1
- CVCL_VU60 26A7
- CVCL_4563 3Y1-B clone 1
- CVCL_VT76 6/9CII
- CVCL_Z425 67j25D
- CVCL_0037 A-431
- CVCL_4367 AH130
- CVCL_4368 AH66-TC
- CVCL_2300 AtT-20
- CVCL_0159 B16-F10
- CVCL_1075 BALL-1
- CVCL_0044 BeWo
- CVCL_1914 BHK-21
- CVCL_RQ70 BHK-21A
- CVCL_LM74 BHK21/13/Py6
- CVCL_6370 BHK570
- CVCL_Z633 BM-N
- CVCL_4565 BRL
- CVCL_0179 BT-474
- CVCL_C190 BTI-Tn-5B1-4
- CVCL_3896 BW5147
- CVCL_VT60 BW5147.PHAR2.7
- CVCL_4724 C-1300 clone N18
- CVCL_VU14 C-1300 clone S20
- CVCL_5245 C10
- CVCL_6550 C127
- CVCL_0194 C6
- CVCL_Z230 C6/36
- CVCL_0025 Caco-2
- CVCL_0207 CCRF-CEM
- CVCL_1859 CCRF-HSB-2 (problematic)
- CVCL_6D96 CE
- CVCL_0213 CHO
- CVCL_VU04 CHO 15B
- CVCL_VU03 CHO B8-300
- CVCL_VU65 CHO E1a
- CVCL_4382 CHO Pro-5
- CVCL_7180 CHO-DG44
- CVCL_1977 CHO-DXB11
- CVCL_0214 CHO-K1
- CVCL_7183 CHO-S
- CVCL_D102 Co115
- CVCL_0218 COLO 205
- CVCL_1989 COLO 320
- CVCL_0223 COS-1
- CVCL_0224 COS-7
- CVCL_0229 CV-1
- CVCL_2434 Detroit 551
- CVCL_8190 Detroit 98/AH-2 (problematic)
- CVCL_0248 DLD-1
- CVCL_3506 EHS
- CVCL_0255 EL4
- CVCL_A1LI Eveline
- CVCL_1905 FL (problematic)
- CVCL_D603 FreeStyle 293-F
- CVCL_4212 H5
- CVCL_1240 H9
- CVCL_4362 HBL-100 (problematic)
- CVCL_0291 HCT 116
- CVCL_0292 HCT 15
- CVCL_2478 HCT 8
- CVCL_M624 HEK (problematic)
- CVCL_0045 HEK293
- CVCL_6974 HEK293-EBNA
- CVCL_6642 HEK293-F
- CVCL_4V95 HEK293SF-3F6
- CVCL_0063 HEK293T
- CVCL_0030 HeLa
- CVCL_1906 HEp-2 (problematic)
- CVCL_0027 Hep-G2 (problematic)
- CVCL_0002 HL-60
- CVCL_3317 HMCB
- CVCL_0317 HT-1080
- CVCL_0320 HT-29
- CVCL_A8EZ HT29
- CVCL_C763 HT29-16E
- CVCL_2959 HUVEC-C
- CVCL_VU61 Hybrid 27-1
- CVCL_VT63 IM4
- CVCL_VT64 IM4/IV
- CVCL_VT67 IM4/V/IV
- CVCL_VT68 IM4/V/IV-G1
- CVCL_VT69 IM4/V/IV-G2
- CVCL_VT70 IM4/V/IV-G3
- CVCL_VT71 IM4/V/IV-G4
- CVCL_VT72 IM4/V/IV-G5
- CVCL_VT65 IM4/Vh
- CVCL_VT66 IM4/Vm
- CVCL_C411 IZD-MB-0503
- CVCL_3949 J558L
- CVCL_0363 JEG-3
- CVCL_0065 Jurkat
- CVCL_0004 K-562
- CVCL_1331 KM12
- CVCL_3440 Lec1
- CVCL_VU62 LEC14
- CVCL_VU63 LEC18
- CVCL_3442 Lec2
- CVCL_VU64 Lec23
- CVCL_3443 Lec8
- CVCL_4358 LL/2 (LLC1)
- CVCL_0391 LLC-PK1
- CVCL_0399 LOVO
- CVCL_1384 LS174T
- CVCL_0397 LS180
- CVCL_1385 LS411N
- CVCL_Z354 LSTM-AA-20A
- CVCL_R978 LTK
- CVCL_0031 MCF-7
- CVCL_0062 MDA-MB-231
- CVCL_8645 MTSV1-7
- CVCL_0593 Mv1Lu
- CVCL_Z591 MYP30
- CVCL_0067 Namalwa
- CVCL_3553 NB41A3
- CVCL_3042 NC-37 (problematic)
- CVCL_1600 NCI-H929
- CVCL_0470 Neuro-2a
- CVCL_0594 NIH 3T3
- CVCL_3758 NRK
- CVCL_3758 NRK
- CVCL_3940 NS0
- CVCL_0465 OVCAR-3
- CVCL_3411 P3X63Ag8
- CVCL_3412 P3X63Ag8U.1
- CVCL_DD11 PIR-P3
- CVCL_IQ79 PIR-P8
- CVCL_0492 Rat1
- CVCL_0504 RKO
- CVCL_2710 RPMI-1788
- CVCL_4698 S2
- CVCL_Z232 Schneider 2
- CVCL_0518 Sf21
- CVCL_0549 Sf9
- CVCL_0033 SK-BR-3
- CVCL_2199 Sp2/0-Ag14
- CVCL_VT74 Sp2/HL-BU
- CVCL_VT62 SPC-Mb-92-C6
- CVCL_0544 SW1116
- CVCL_3885 SW1398
- CVCL_1718 SW1463
- CVCL_1724 SW48
- CVCL_0546 SW480
- CVCL_0547 SW620
- CVCL_1729 SW837
- CVCL_0632 SW948
- CVCL_0553 T-47D
- CVCL_0555 T84
- CVCL_4321 TA3/Ha
- CVCL_0577 WEHI-231
- CVCL_2760 WiDr
- CVCL_1D00 Zajdela-Hepatoma
- CVCL_0588 ZR-75-1
Help
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:
Residue type | Short name | Abbreviated code | Condensed code |
Monosaccharide | Hexose | Hex | H |
Monosaccharide | N-Acetylhexosamine | HexNAc | N |
Monosaccharide | Deoxyhexose | dHex | F |
Monosaccharide | N-Acetylneuraminic acid | NeuAc | S |
Monosaccharide | N-Glycolylneuraminic acid | NeuGc | G |
Monosaccharide | Pentose | Pent | P |
Monosaccharide | Hexuronic acid | HexA | A |
Monosaccharide | Ketodeoxyoctonic acid | Kdn | K |
Monosaccharide | Ketodeoxynononic acid | Kdo | O |
Substituent | Acetyl | Ac | a |
Substituent | Methyl | Me | m |
Substituent | Phosphate | Ph | p |
Substituent | Sulfate | Su | s |
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:
- It does not already exist in the graph
- 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:
Residue | HexNAc | Hex | Fuc | NeuAc | NeuGc | Su |
Colour | blue | green | red | purple | orange | magenta |