KPV - KEGG Pathway Viewer
by Igor Brandão

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In the table below, you'll find the most used terms in this tool:

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.

00380 Tryptophan metabolism
Metabolism; Amino acid metabolism

62
NODES

62
EDGES

4713
ORGANISMS

9
COMMUNITIES

2.0000
AVG. DEGREE

0.0009
AVG. BETWEENNESS

29
ARTICULATION POINTS

33
OTHER NODES

Filters

Note: Just working for ec, hsa & mmu organisms.

Pathway Viewer

Pathway details

Network metrics

Nodes	Edges
62	62

Articulation point with highest impact	Disconnected nodes when remove it
ec:4.1.1.28_1	16

Global metrics
Communities	Avg. degree	Avg. betweenness
9	2.0000	0.0009

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
29	10	12	33

Description

Class

Metabolism; Amino acid metabolism

Map

Tryptophan metabolism

Module

Melatonin biosynthesis, tryptophan => serotonin => melatonin [PATH:map00380], Tryptophan metabolism, tryptophan => kynurenine => 2-aminomuconate [PATH:map00380], Glucosinolate biosynthesis, tryptophan => glucobrassicin [PATH:map00380]

Associated diseases

Glutaric acidemia, Acatalasemia, Brunner syndrome, Delayed sleep phase syndrome, Aromatic L-amino acid decarboxylase deficiency, Primary congenital glaucoma, 3-Hydroxyacyl-CoA dehydrogenase deficiency, Hydroxykynureninuria, Vertebral, cardiac, renal, and limb defects syndrome

Associated organisms count

Total organisms
4713

Eukaryotes	Prokaryotes
521	4192

Animals	Plants	Fungi	Protists	Bacteria	Archaea
248	105	123	45	3956	236

GO associated terms

GO: 0006568 0009851

KO pathway

ko00380

References

list(REFERENCE = "PMID:15749753", AUTHORS = "Woodward AW, Bartel B", TITLE = "Auxin: regulation, action, and interaction.", JOURNAL = c("Ann Bot 95:707-35 (2005)", "DOI:10.1093/aob/mci083"))