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.

00621 Dioxin degradation
Metabolism; Xenobiotics biodegradation and metabolism

Dioxins and dioxin-like compounds, including PCDDs, PCDFs and PCBs, are persistent organic pollutants (POPs) that are resistant to environmental degradation. However, POPs can be degraded by certain microorganisms with acquisition of a novel set of enzymes, such as biphenyl degradation by Paraburkholderia xenovorans LB400 involving four novel enzymes encoded in operon-like structures [MD:M00543]. DDT, another POP, and carbazol are also known to be degraded in similar pathways.

Nodes	Edges
14	12

Articulation point with highest impact	Disconnected nodes when remove it
ec:4.2.1.80	4

Global metrics
4	1.7143	0.0096

Nodes classification
8	1	3	6

Total organisms
1104

Eukaryotes	Prokaryotes
0	1104

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	1100	4

list(REFERENCE = "PMID:12450109", AUTHORS = "Nojiri H, Omori T.", TITLE = "Molecular bases of aerobic bacterial degradation of dioxins: involvement of angular dioxygenation.", JOURNAL = c("Biosci Biotechnol Biochem 66:2001-16 (2002)", "DOI:10.1271/bbb.66.2001")), list(REFERENCE = "PMID:16775784", AUTHORS = "Jin S, Zhu T, Xu X, Xu Y.", TITLE = "Biodegradation of dibenzofuran by Janibacter terrae strain XJ-1.", JOURNAL = c("Curr Microbiol 53:30-6 (2006)", "DOI:10.1007/s00284-005-0180-1")), list(REFERENCE = "PMID:12483604", AUTHORS = "Nojiri H, Habe H, Omori T.", TITLE = "Bacterial degradation of aromatic compounds via angular dioxygenation.", JOURNAL = c("J Gen Appl Microbiol 47:279-305 (2001)", "DOI:10.2323/jgam.47.279")), list(REFERENCE = "PMID:11322788", AUTHORS = "Kasuga K, Habe H, Chung JS, Yoshida T, Nojiri H, Yamane H, Omori T.", TITLE = "Isolation and characterization of the genes encoding a novel oxygenase component of angular dioxygenase from the gram-positive dibenzofuran-degrader Terrabacter sp. strain DBF63.", JOURNAL = c("Biochem Biophys Res Commun 283:195-204 (2001)", "DOI:10.1006/bbrc.2001.4763")), list(REFERENCE = "PMID:17142386", AUTHORS = "Vezina J, Barriault D, Sylvestre M", TITLE = "Family shuffling of soil DNA to change the regiospecificity of Burkholderia xenovorans LB400 biphenyl dioxygenase.", JOURNAL = c("J Bacteriol 189:779-88 (2007)", "DOI:10.1128/JB.01267-06")), list(REFERENCE = "PMID:12501294", AUTHORS = "Ouchiyama N, Miyachi S, Omori T", TITLE = "Cloning and nucleotide sequence of carbazole catabolic genes from Pseudomonas stutzeri strain OM1, isolated from activated sludge.", JOURNAL = c("J Gen Appl Microbiol 44:57-63 (1998)", "DOI:10.2323/jgam.44.57")), list(REFERENCE = "PMID:9244273", AUTHORS = "Sato SI, Ouchiyama N, Kimura T, Nojiri H, Yamane H, Omori T", TITLE = "Cloning of genes involved in carbazole degradation of Pseudomonas sp. strain CA10: nucleotide sequences of genes and characterization of meta-cleavage enzymes and hydrolase.", JOURNAL = c("J Bacteriol 179:4841-9 (1997)", "DOI:10.1128/JB.179.15.4841-4849.1997")), list(REFERENCE = "PMID:23415487", AUTHORS = "Nguyen PA, Trinh TH, Fukumitsu Y, Shimodaira J, Miyauchi K, Tokuda M, Kasai D, Masai E, Fukuda M", TITLE = "Gene cluster and regulation system for 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE) degradation in Janibacter sp. TYM3221.", JOURNAL = c("J Biosci Bioeng 116:91-100 (2013)", "DOI:10.1016/j.jbiosc.2013.01.007"))

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
8	1	3	6

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00621 Dioxin degradation
Metabolism; Xenobiotics biodegradation and metabolism

14
NODES

12
EDGES

1104
ORGANISMS

4
COMMUNITIES

1.7143
AVG. DEGREE

0.0096
AVG. BETWEENNESS

8
ARTICULATION POINTS

6
OTHER NODES

Filters

Pathway Viewer

14

12

ec:4.2.1.80

4

4

1.7143

0.0096

8

1

3

6

1104

0

1104

0

0

0

0

1100

4

Global metrics
Communities	Avg. degree	Avg. betweenness
4	1.7143	0.0096

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00621 Dioxin degradation Metabolism; Xenobiotics biodegradation and metabolism

14 NODES

12 EDGES

1104 ORGANISMS

4 COMMUNITIES

1.7143 AVG. DEGREE

0.0096 AVG. BETWEENNESS

8 ARTICULATION POINTS

6 OTHER NODES

Filters

Pathway Viewer

14

12

ec:4.2.1.80

4

4

1.7143

0.0096

8

1

3

6

1104

0

1104

0

0

0

0

1100

4

KPV - KEGG Pathway Viewer
by Igor Brandão

00621 Dioxin degradation
Metabolism; Xenobiotics biodegradation and metabolism

14
NODES

12
EDGES

1104
ORGANISMS

4
COMMUNITIES

1.7143
AVG. DEGREE

0.0096
AVG. BETWEENNESS

8
ARTICULATION POINTS

6
OTHER NODES