KPV - KEGG Pathway Viewer

Term	Meaning
Metabolic pathway	In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The term network is sometimes defined to mean a graph in which attributes (e.g. names) are associated with the vertices and edges, and the subject that expresses and understands the real-world systems as a network is called network science.
Network/Graphs	In mathematics, graph theory is the study of graphs, which are mathematical structures used to model pairwise relations between objects.
Network visualization	Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
Node	In mathematics, and more specifically in graph theory, a vertex (plural vertices) or node is the fundamental unit of which graphs are formed.
Edge	For an undirected graph, an unordered pair of nodes that specify a line joining these two nodes are said to form an edge. For a directed graph, the edge is an ordered pair of nodes. The terms "arc," "branch," "line," "link," and "1-simplex" are sometimes used instead of edge.
KEGG	KEGG: Kyoto Encyclopedia of Genes and Genomes is a Japanese database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
KEGG Pathway	KEGG PATHWAY is a collection of manually drawn pathway maps representing the knowledge on the molecular interaction, reaction and relation.
Pathway code	Each pathway map is identified by the combination of 2-4 letter prefix code and 5 digit number.
Articulation point	In a graph, a vertex is called an articulation point if removing it and all the edges associated with it results in the increase of the number of connected components in the graph.
Articulation point impact	The impact is defined as the number of vertices that get disconnected from the main (largest) surviving connected component after the removal of the articulation point node.
AP node	AP is the abbreviation for Articulation point.
HAP node	AP is the abbreviation for Hub and Articulation point.
HUB node	In network science, a hub is a node with a number of links that greatly exceeds the average.
Other nodes	In the context of this tool, other nodes represent nodes without classification.

Nodes	Edges
8	6

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.13.11.80	3

Global metrics
3	1.5000	0.0119

Nodes classification
1	0	2	7

Total organisms
343

Eukaryotes	Prokaryotes
0	343

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	342	1

list(REFERENCE = "PMID:24884615", AUTHORS = "Xu L, Huang H, Wei W, Zhong Y, Tang B, Yuan H, Zhu L, Huang W, Ge M, Yang S, Zheng H, Jiang W, Chen D, Zhao GP, Zhao W", TITLE = "Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis.", JOURNAL = c("BMC Genomics 15:363 (2014)", "DOI:10.1186/1471-2164-15-363")), list(REFERENCE = "PMID:12596194", AUTHORS = "Hubbard BK, Walsh CT.", TITLE = "Vancomycin assembly: nature`s way.", JOURNAL = c("Angew Chem Int Ed Engl 42:730-65 (2003)", "DOI:10.1002/anie.200390202")), list(REFERENCE = "PMID:11035791", AUTHORS = "Chen H, Thomas MG, Hubbard BK, Losey HC, Walsh CT, Burkart MD.", TITLE = "Deoxysugars in glycopeptide antibiotics: enzymatic synthesis of TDP-L-epivancosamine in chloroeremomycin biosynthesis.", JOURNAL = c("Proc Natl Acad Sci U S A 97:11942-7 (2000)", "DOI:10.1073/pnas.210395097")), list(REFERENCE = "PMID:9545426", AUTHORS = "van Wageningen AM, Kirkpatrick PN, Williams DH, Harris BR, Kershaw JK, Lennard NJ, Jones M, Jones SJ, Solenberg PJ.", TITLE = "Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic.", JOURNAL = c("Chem Biol 5:155-62 (1998)", "DOI:10.1016/S1074-5521(98)90060-6"))

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
1	0	2	7

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

01055 Biosynthesis of vancomycin group antibiotics
Metabolism; Metabolism of terpenoids and polyketides

8
NODES

6
EDGES

343
ORGANISMS

3
COMMUNITIES

1.5000
AVG. DEGREE

0.0119
AVG. BETWEENNESS

1
ARTICULATION POINTS

7
OTHER NODES

Filters

Pathway Viewer

8

6

ec:1.13.11.80

3

3

1.5000

0.0119

1

0

2

7

343

0

343

0

0

0

0

342

1

Global metrics
Communities	Avg. degree	Avg. betweenness
3	1.5000	0.0119

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

01055 Biosynthesis of vancomycin group antibiotics Metabolism; Metabolism of terpenoids and polyketides

8 NODES

6 EDGES

343 ORGANISMS

3 COMMUNITIES

1.5000 AVG. DEGREE

0.0119 AVG. BETWEENNESS

1 ARTICULATION POINTS

7 OTHER NODES