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.

00950 Isoquinoline alkaloid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Isoquinoline alkaloids are tyrosine-derived plant alkaloids with an isoquinoline skeleton. Among them benzylisoquinoline alkaloids form an important group with potent pharmacological activity, including analgesic compounds of morphine and codeine, and anti-infective agents of berberine, palmatine, and magnoflorine. Biosynthesis of isoquinoline alkaloids proceeds via decarboxylation of tyrosine or DOPA to yield dopamine, which together with 4-hydroxyphenylacetaldehyde, an aldehyde derived from tyrosine, is converted to reticuline, an important precursor of various benzylisoquinoline alkaloids.

Nodes	Edges
77	90

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.21.3.3	39

Global metrics
13	2.3377	0.0115

Nodes classification
27	4	15	50

Total organisms
105

Eukaryotes	Prokaryotes
105	0

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	105	0	0	0	0

list(REFERENCE = "PMID:10811648", AUTHORS = "Morishige T, Tsujita T, Yamada Y, Sato F", TITLE = "Molecular characterization of the S-adenosyl-L-methionine:3`-hydroxy-N-methylcoclaurine 4`-O-methyltransferase involved in isoquinoline alkaloid biosynthesis in Coptis japonica.", JOURNAL = c("J Biol Chem 275:23398-405 (2000)", "DOI:10.1074/jbc.M002439200")), list(REFERENCE = "PMID:12423366", AUTHORS = "Morishige T, Dubouzet E, Choi KB, Yazaki K, Sato F", TITLE = "Molecular cloning of columbamine O-methyltransferase from cultured Coptis japonica cells.", JOURNAL = c("Eur J Biochem 269:5659-67 (2002)", "DOI:10.1046/j.1432-1033.2002.03275.x")), list(REFERENCE = "PMID:14675446", AUTHORS = "Ounaroon A, Decker G, Schmidt J, Lottspeich F, Kutchan TM", TITLE = "(R,S)-Reticuline 7-O-methyltransferase and (R,S)-norcoclaurine 6-O-methyltransferase of Papaver somniferum - cDNA cloning and characterization of methyl transfer enzymes of alkaloid biosynthesis in opium poppy.", JOURNAL = c("Plant J 36:808-19 (2003)", "DOI:10.1046/j.1365-313X.2003.01928.x")), list(REFERENCE = "PMID:18230623", AUTHORS = "Ikezawa N, Iwasa K, Sato F", TITLE = "Molecular cloning and characterization of CYP80G2, a cytochrome P450 that catalyzes an intramolecular C-C phenol coupling of (S)-reticuline in magnoflorine biosynthesis, from cultured Coptis japonica cells.", JOURNAL = c("J Biol Chem 283:8810-21 (2008)", "DOI:10.1074/jbc.M705082200")), list(REFERENCE = "PMID:18476877", AUTHORS = "Facchini PJ, De Luca V", TITLE = "Opium poppy and Madagascar periwinkle: model non-model systems to investigate alkaloid biosynthesis in plants.", JOURNAL = c("Plant J 54:763-84 (2008)", "DOI:10.1111/j.1365-313X.2008.03438.x")), list(REFERENCE = "PMID:18492807", AUTHORS = "Minami H, Kim JS, Ikezawa N, Takemura T, Katayama T, Kumagai H, Sato F", TITLE = "Microbial production of plant benzylisoquinoline alkaloids.", JOURNAL = c("Proc Natl Acad Sci U S A 105:7393-8 (2008)", "DOI:10.1073/pnas.0802981105")), list(REFERENCE = "", AUTHORS = "Rueffer M, Bauer W, Zenk MH.", TITLE = "The formation of corydaline and related alkaloids in Corydalis cava in vivo and in vitro.", JOURNAL = c("Can J Chem 72:170-175 (1994)", "DOI:10.1139/v94-026")), list(REFERENCE = "", AUTHORS = "Sekine Y, Crevelling C, Bell M, Brossi A.", TITLE = "Mammalian alkaloids: O-methylation of (+-)-norcoclaurine-1-carboxylic acid and related isoquinolines including (S)- and (R)-norcoclaurine with 14C-labeled S-adenosyl-L-methionine in presence of mammalian catechol O-methyltransferase.", JOURNAL = c("Helvetica Chimica Acta 73(2):426-432 (1990)", "DOI:10.1002/hlca.19900730222")), list(REFERENCE = "", AUTHORS = "De-Eknamkul W, Tanahashi T, Zenk MH.", TITLE = "Enzymic 10-hydroxylation and 10-O-methylation of dihydrosanguinarine in dihydrochelirubine formation by Eschscholtzia.", JOURNAL = c("Phytochemistry 31(8):2713-2717 (1992)", "DOI:10.1016/0031-9422(92)83617-8")), list(REFERENCE = "", AUTHORS = "Kammerer L, De-Eknamkul W, Zenk MH.", TITLE = "Enzymic 12-hydroxylation and 12-O-methylation of dihydrochelirubine in dihydromacarpine formation by Thalictrum bulgaricum.", JOURNAL = c("Phytochemistry 36(6):1409-1416 (1994)", "DOI:10.1016/S0031-9422(00)89732-0")), list(REFERENCE = "PMID:24241413", AUTHORS = "Schumacher HM, Zenk MH", TITLE = "Partial purification and characterization of dihydrobenzophenanthridine oxidase from Eschscholtzia californica cell suspension cultures.", JOURNAL = c("Plant Cell Rep 7:43-6 (1988)", "DOI:10.1007/BF00272975")), list(REFERENCE = "", AUTHORS = "Rueffer M, Zenk MH.", TITLE = "Enzymatic formation of protopines by a microsomal cytochrome P-450 system of Corydalis vaginans.", JOURNAL = c("Tetrahedron Letters 28(44):5307-5310 (1987)", "DOI:10.1016/S0040-4039(00)96715-7"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00950 Isoquinoline alkaloid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

77
NODES

90
EDGES

105
ORGANISMS

13
COMMUNITIES

2.3377
AVG. DEGREE

0.0115
AVG. BETWEENNESS

27
ARTICULATION POINTS

50
OTHER NODES

Filters

Pathway Viewer

77

90

ec:1.21.3.3

39

13

2.3377

0.0115

27

4

15

50

105

105

0

0

105

0

0

0

0

Global metrics
Communities	Avg. degree	Avg. betweenness
13	2.3377	0.0115

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00950 Isoquinoline alkaloid biosynthesis Metabolism; Biosynthesis of other secondary metabolites

77 NODES

90 EDGES

105 ORGANISMS

13 COMMUNITIES

2.3377 AVG. DEGREE

0.0115 AVG. BETWEENNESS

27 ARTICULATION POINTS

50 OTHER NODES