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.

Network metrics

Nodes	Edges
2	1

Articulation point with highest impact	Disconnected nodes when remove it
NA	1

Global metrics
Communities	Avg. degree	Avg. betweenness
2	1.0000	-1.0000

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

Brassinosteroids are a group of plant steroid hormones that regulate growth and development. More than fifty naturally occurring brassinosteroids have been identified in a wide range of plant species. The most abundant and widely occurring brassinosteroids are C28 steroids, and among them brassinolide (BL) is the most biologically active. Plants have multiple pathways for biosynthesis of BL, which are derived from the steroid biosynthetic pathway. Two pathways from campestanol to castasterone (CS), C6 oxidation and the late-C6 oxidation pathways, operate in many plants. Another branching pathway, the early-C22 oxidation pathway, was demonstrated using a brassinosteroid-deficient mutant of Arabidopsis thaliana. Recently, a new shortcut pathway from campesterol to 6-deoxotyphasterol was demonstrated by a functional analysis of cytochrome P450 monooxygenases responsible for brassinosteroid biosynthesis. Thus, at least four pathways are involved in the biosynthesis of CS, and CS is further metabolized to BL by lactonization of the B ring.

Class

Metabolism; Metabolism of terpenoids and polyketides

Map

Brassinosteroid biosynthesis

Module

Castasterone biosynthesis, campesterol => castasterone [PATH:map00905]

Associated diseases

Associated organisms count

Total organisms
91

Eukaryotes	Prokaryotes
91	0

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	91	0	0	0	0

GO associated terms

GO: 0016132

KO pathway

ko00905

References

list(REFERENCE = "", AUTHORS = "Koshiba K, Kamiya Y.", TITLE = "[Atarasii Syokubutuhorumon no Kagaku] (In Japanese)", JOURNAL = "Koudansya saientific:199-138 (2002)"), list(REFERENCE = "", AUTHORS = "Fukuda H, Matida Y, Kamiya Y, Kakimoto T.", TITLE = "[Shinpan Syokubutuhorumon no Sigunarudentatu] (In Japanese)", JOURNAL = "Syujyunsya:165-186 (2004)"), list(REFERENCE = "PMID:12529536", AUTHORS = "Shimada Y, Goda H, Nakamura A, Takatsuto S, Fujioka S, Yoshida S.", TITLE = "Organ-specific expression of brassinosteroid-biosynthetic genes and distribution of endogenous brassinosteroids in Arabidopsis.", JOURNAL = c("Plant Physiol 131:287-97 (2003)", "DOI:10.1104/pp.013029")), list(REFERENCE = "", AUTHORS = "Choe, S.", TITLE = "Brassinosteroid biosynthesis and inactivation.", JOURNAL = "Physiologia Plantarum 126:539-548 (2006)"), list(REFERENCE = "PMID:17138693", AUTHORS = "Ohnishi T, Szatmari AM, Watanabe B, Fujita S, Bancos S, Koncz C, Lafos M, Shibata K, Yokota T, Sakata K, Szekeres M, Mizutani M", TITLE = "C-23 hydroxylation by Arabidopsis CYP90C1 and CYP90D1 reveals a novel shortcut in brassinosteroid biosynthesis.", JOURNAL = c("Plant Cell 18:3275-88 (2006)", "DOI:10.1105/tpc.106.045443")), list(REFERENCE = "PMID:17693126", AUTHORS = "Bishop GJ", TITLE = "Refining the plant steroid hormone biosynthesis pathway.", JOURNAL = c("Trends Plant Sci 12:377-80 (2007)", "DOI:10.1016/j.tplants.2007.07.001")), list(REFERENCE = "PMID:15710611", AUTHORS = "Nomura T, Kushiro T, Yokota T, Kamiya Y, Bishop GJ, Yamaguchi S", TITLE = "The last reaction producing brassinolide is catalyzed by cytochrome P-450s, CYP85A3 in tomato and CYP85A2 in Arabidopsis.", JOURNAL = c("J Biol Chem 280:17873-9 (2005)", "DOI:10.1074/jbc.M414592200")), list(REFERENCE = "PMID:18685225", AUTHORS = "Katsumata T, Hasegawa A, Fujiwara T, Komatsu T, Notomi M, Abe H, Natsume M, Kawaide H", TITLE = "Arabidopsis CYP85A2 catalyzes lactonization reactions in the biosynthesis of 2-deoxy-7-oxalactone brassinosteroids.", JOURNAL = c("Biosci Biotechnol Biochem 72:2110-7 (2008)", "DOI:10.1271/bbb.80192")), list(REFERENCE = "PMID:15705958", AUTHORS = "Tanabe S, Ashikari M, Fujioka S, Takatsuto S, Yoshida S, Yano M, Yoshimura A, Kitano H, Matsuoka M, Fujisawa Y, Kato H, Iwasaki Y", TITLE = "A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length.", JOURNAL = c("Plant Cell 17:776-90 (2005)", "DOI:10.1105/tpc.104.024950")), list(REFERENCE = "PMID:14615594", AUTHORS = "Hong Z, Ueguchi-Tanaka M, Umemura K, Uozu S, Fujioka S, Takatsuto S, Yoshida S, Ashikari M, Kitano H, Matsuoka M", TITLE = "A rice brassinosteroid-deficient mutant, ebisu dwarf (d2), is caused by a loss of function of a new member of cytochrome P450.", JOURNAL = c("Plant Cell 15:2900-10 (2003)", "DOI:10.1105/tpc.014712"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00905 Brassinosteroid biosynthesis
Metabolism; Metabolism of terpenoids and polyketides

2
NODES

1
EDGES

91
ORGANISMS

2
COMMUNITIES

1.0000
AVG. DEGREE

-1.0000
AVG. BETWEENNESS

0
ARTICULATION POINTS

2
OTHER NODES

Filters

Pathway Viewer

2

1

NA

1

2

1.0000

-1.0000

0

0

0

2

91

91

0

0

91

0

0

0

0

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00905 Brassinosteroid biosynthesis Metabolism; Metabolism of terpenoids and polyketides

2 NODES

1 EDGES

91 ORGANISMS

2 COMMUNITIES

1.0000 AVG. DEGREE

-1.0000 AVG. BETWEENNESS

0 ARTICULATION POINTS

2 OTHER NODES