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.

00970 Aminoacyl-tRNA biosynthesis
Aminoacyl-tRNA biosynthesis

Genetic Information Processing; Translation

12
NODES

7
EDGES

6112
ORGANISMS

5
COMMUNITIES

1.1667
AVG. DEGREE

0.0008
AVG. BETWEENNESS

2
ARTICULATION POINTS

10
OTHER NODES

Filters

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

Pathway Viewer

Pathway details

Network metrics

Nodes	Edges
12	7

Articulation point with highest impact	Disconnected nodes when remove it
ec:6.1.1.11_1, ec:2.7.1.164	2

Global metrics
Communities	Avg. degree	Avg. betweenness
5	1.1667	0.0008

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
2	2	2	10

Description

Genetic Information Processing; Translation

Class

Aminoacyl-tRNA biosynthesis

Map

Charcot-Marie-Tooth disease, Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation, Pontocerebellar hypoplasia, Myopathy with lactic acidosis and sideroblastic anaemia, MELAS Syndrome, Spastic ataxia, Myoclonic Epilepsy and Ragged-Red Fiber Disease, Infantile liver failure, Perrault syndrome, CAGSSS syndrome

Module

Associated diseases

Associated organisms count

Total organisms
6112

Eukaryotes	Prokaryotes
531	5581

Animals	Plants	Fungi	Protists	Bacteria	Archaea
248	105	128	50	5282	299

GO associated terms

KO pathway

ko00970

References

list(REFERENCE = "PMID:18252769", AUTHORS = "Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, Soll D", TITLE = "From one amino acid to another: tRNA-dependent amino acid biosynthesis.", JOURNAL = c("Nucleic Acids Res 36:1813-25 (2008)", "DOI:10.1093/nar/gkn015")), list(REFERENCE = "PMID:15314242", AUTHORS = "Polycarpo C, Ambrogelly A, Berube A, Winbush SM, McCloskey JA, Crain PF, Wood JL, Soll D", TITLE = "An aminoacyl-tRNA synthetase that specifically activates pyrrolysine.", JOURNAL = c("Proc Natl Acad Sci U S A 101:12450-4 (2004)", "DOI:10.1073/pnas.0405362101"))