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.

00941 Flavonoid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Flavonoids are a major class of plant secondary metabolites that serves a multitude of functions including pigments and antioxidant activity. Flavonoids are synthesized from phenylpropanoid derivatives by condensation with malonyl-CoA. For example, condensation of p-coumaroyl-CoA (C6-C3) with three malonyl-CoA (C3) molecules results in naringenin chalcone with a diphenylpropane (C6-C3-C6) unit, which is converted to naringenin with the flavone (2-phenylchromen-4-one) backbone by conjugate ring closure. These and further modifications yield a variety of structural forms including chalcones, flavanones, dihyroflavonols, and flavans, anthocyanins, flavones and flavonols, and isoflavonoids.

Nodes	Edges
76	86

Articulation point with highest impact	Disconnected nodes when remove it
ec:5.5.1.6	32

Global metrics
10	2.2632	0.0016

Nodes classification
28	14	15	48

Total organisms
92

Eukaryotes	Prokaryotes
92	0

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	92	0	0	0	0

list(REFERENCE = "PMID:16945088", AUTHORS = "Tsai CJ, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y.", TITLE = "Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus.", JOURNAL = c("New Phytol 172:47-62 (2006)", "DOI:10.1111/j.1469-8137.2006.01798.x")), list(REFERENCE = "PMID:16367960", AUTHORS = "Ono E, Hatayama M, Isono Y, Sato T, Watanabe R, Yonekura-Sakakibara K, Fukuchi-Mizutani M, Tanaka Y, Kusumi T, Nishino T, Nakayama T.", TITLE = "Localization of a flavonoid biosynthetic polyphenol oxidase in vacuoles.", JOURNAL = c("Plant J 45:133-43 (2006)", "DOI:10.1111/j.1365-313X.2005.02625.x")), list(REFERENCE = "PMID:16774647", AUTHORS = "Morreel K, Goeminne G, Storme V, Sterck L, Ralph J, Coppieters W, Breyne P, Steenackers M, Georges M, Messens E, Boerjan W.", TITLE = "Genetical metabolomics of flavonoid biosynthesis in Populus: a case study.", JOURNAL = c("Plant J 47:224-37 (2006)", "DOI:10.1111/j.1365-313X.2006.02786.x")), list(REFERENCE = "PMID:16832053", AUTHORS = "Ono E, Fukuchi-Mizutani M, Nakamura N, Fukui Y, Yonekura-Sakakibara K, Yamaguchi M, Nakayama T, Tanaka T, Kusumi T, Tanaka Y.", TITLE = "Yellow flowers generated by expression of the aurone biosynthetic pathway.", JOURNAL = c("Proc Natl Acad Sci U S A 103:11075-80 (2006)", "DOI:10.1073/pnas.0604246103")), list(REFERENCE = "", AUTHORS = "Halbwirth H, Martens S, Wienand U, Forkmann G, Stich K.", TITLE = "Synthesis of (14C)-labeled 5-deoxyflavonoids and their application in the study of dihydroflavonol/leucoanthocyanidin interconversion by dihydroflavonol 4-reductase.", JOURNAL = c("Plant Science 170(3): 587-595 (2006)", "DOI:10.1016/j.plantsci.2005.10.013")), list(REFERENCE = "PMID:15231405", AUTHORS = "Stevens JF, Page JE.", TITLE = "Xanthohumol and related prenylflavonoids from hops and beer: to your good health!", JOURNAL = c("Phytochemistry 65:1317-30 (2004)", "DOI:10.1016/j.phytochem.2004.04.025")), list(REFERENCE = "", AUTHORS = "Ogata J, Itoh Y, Ishida M, Yoshida H, Ozeki Y.", TITLE = "Cloning and heterologous expression of cDNAs encoding flavonoid glucosyltransferases from Dianthus caryophyllus.", JOURNAL = c("Plant Biotechnology 21(5):367-375 (2004)", "DOI:10.5511/plantbiotechnology.21.367")), list(REFERENCE = "PMID:12828368", AUTHORS = "Springob K, Nakajima J, Yamazaki M, Saito K.", TITLE = "Recent advances in the biosynthesis and accumulation of anthocyanins.", JOURNAL = c("Nat Prod Rep 20:288-303 (2003)", "DOI:10.1039/b109542k")), list(REFERENCE = "PMID:12644647", AUTHORS = "Shimada N, Aoki T, Sato S, Nakamura Y, Tabata S, Ayabe S.", TITLE = "A cluster of genes encodes the two types of chalcone isomerase involved in the biosynthesis of general flavonoids and legume-specific 5-deoxy(iso)flavonoids in Lotus japonicus.", JOURNAL = c("Plant Physiol 131:941-51 (2003)", "DOI:10.1104/pp.004820")), list(REFERENCE = "", AUTHORS = "Halbwirth H, Martens S, Wienand U, Forkmann G, Stich K.", TITLE = "Biochemical formation of anthocyanins in silk tissue of Zea mays.", JOURNAL = c("Plant Science 164(4):489-495 (2003)", "DOI:10.1016/S0168-9452(02)00433-8")), list(REFERENCE = "", AUTHORS = "Martens S, Knott J, Seitz CA, Janvari L, Yu SN, Forkmann G.", TITLE = "Impact of biochemical pre-studies on specific metabolic engineering strategies of flavonoid biosynthesis in plant tissues.", JOURNAL = c("Biochemical Engineering Journal 14(3):227-235 (2003)", "DOI:10.1016/S1369-703X(02)00224-3")), list(REFERENCE = "PMID:11073455", AUTHORS = "Nakayama T, Yonekura-Sakakibara K, Sato T, Kikuchi S, Fukui Y, Fukuchi-Mizutani M, Ueda T, Nakao M, Tanaka Y, Kusumi T, Nishino T.", TITLE = "Aureusidin synthase: a polyphenol oxidase homolog responsible for flower coloration.", JOURNAL = c("Science 290:1163-6 (2000)", "DOI:10.1126/science.290.5494.1163")), list(REFERENCE = "PMID:16667183", AUTHORS = "Lewinsohn E, Britsch L, Mazur Y, Gressel J", TITLE = "Flavanone Glycoside Biosynthesis in Citrus: Chalcone Synthase, UDP-Glucose:Flavanone-7-O-Glucosyl-Transferase and -Rhamnosyl-Transferase Activities in Cell-Free Extracts.", JOURNAL = c("Plant Physiol 91:1323-8 (1989)", "DOI:10.1104/pp.91.4.1323"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00941 Flavonoid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

76
NODES

86
EDGES

92
ORGANISMS

10
COMMUNITIES

2.2632
AVG. DEGREE

0.0016
AVG. BETWEENNESS

28
ARTICULATION POINTS

48
OTHER NODES

Filters

Pathway Viewer

76

86

ec:5.5.1.6

32

10

2.2632

0.0016

28

14

15

48

92

92

0

0

92

0

0

0

0

Global metrics
Communities	Avg. degree	Avg. betweenness
10	2.2632	0.0016

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00941 Flavonoid biosynthesis Metabolism; Biosynthesis of other secondary metabolites

76 NODES

86 EDGES

92 ORGANISMS

10 COMMUNITIES

2.2632 AVG. DEGREE

0.0016 AVG. BETWEENNESS

28 ARTICULATION POINTS

48 OTHER NODES