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.

00940 Phenylpropanoid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Phenylpropanoids are a group of plant secondary metabolites derived from phenylalanine and having a wide variety of functions both as structural and signaling molecules. Phenylalanine is first converted to cinnamic acid by deamination. It is followed by hydroxylation and frequent methylation to generate coumaric acid and other acids with a phenylpropane (C6-C3) unit. Reduction of the CoA-activated carboxyl groups of these acids results in the corresponding aldehydes and alcohols. The alcohols are called monolignols, the starting compounds for biosynthesis of lignin.

Nodes	Edges
64	85

Articulation point with highest impact	Disconnected nodes when remove it
ec:2.3.1.133_1	19

Global metrics
11	2.6563	0.0043

Nodes classification
12	4	13	52

Total organisms
97

Eukaryotes	Prokaryotes
97	0

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	97	0	0	0	0

list(REFERENCE = "PMID:14729911", AUTHORS = "Nair RB, Bastress KL, Ruegger MO, Denault JW, Chapple C.", TITLE = "The Arabidopsis thaliana REDUCED EPIDERMAL FLUORESCENCE1 gene encodes an aldehyde dehydrogenase involved in ferulic acid and sinapic acid biosynthesis.", JOURNAL = c("Plant Cell 16:544-54 (2004)", "DOI:10.1105/tpc.017509")), list(REFERENCE = "PMID:14551235", AUTHORS = "Baucher M, Halpin C, Petit-Conil M, Boerjan W.", TITLE = "Lignin: genetic engineering and impact on pulping.", JOURNAL = c("Crit Rev Biochem Mol Biol 38:305-50 (2003)", "DOI:10.1080/10409230391036757")), list(REFERENCE = "PMID:15878986", AUTHORS = "Rogers LA, Dubos C, Cullis IF, Surman C, Poole M, Willment J, Mansfield SD, Campbell MM.", TITLE = "Light, the circadian clock, and sugar perception in the control of lignin biosynthesis.", JOURNAL = c("J Exp Bot 56:1651-63 (2005)", "DOI:10.1093/jxb/eri162")), list(REFERENCE = "PMID:12242395", AUTHORS = "Whetten R, Sederoff R.", TITLE = "Lignin Biosynthesis.", JOURNAL = c("Plant Cell 7:1001-1013 (1995)", "DOI:10.1105/tpc.7.7.1001")), list(REFERENCE = "PMID:8972602", AUTHORS = "Lorenzen M, Racicot V, Strack D, Chapple C.", TITLE = "Sinapic acid ester metabolism in wild type and a sinapoylglucose-accumulating mutant of arabidopsis.", JOURNAL = c("Plant Physiol 112:1625-30 (1996)", "DOI:10.1104/pp.112.4.1625")), list(REFERENCE = "PMID:1477555", AUTHORS = "Chapple CC, Vogt T, Ellis BE, Somerville CR.", TITLE = "An Arabidopsis mutant defective in the general phenylpropanoid pathway.", JOURNAL = c("Plant Cell 4:1413-24 (1992)", "DOI:10.1105/tpc.4.11.1413")), list(REFERENCE = "PMID:14612585", AUTHORS = "Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W.", TITLE = "Genome-wide characterization of the lignification toolbox in Arabidopsis.", JOURNAL = c("Plant Physiol 133:1051-71 (2003)", "DOI:10.1104/pp.103.026484")), list(REFERENCE = "PMID:14568076", AUTHORS = "Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG.", TITLE = "An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof.", JOURNAL = c("Phytochemistry 64:1097-112 (2003)", "DOI:10.1016/S0031-9422(03)00517-X")), list(REFERENCE = "PMID:10934215", AUTHORS = "Meyermans H, Morreel K, Lapierre C, Pollet B, De Bruyn A, Busson R, Herdewijn P, Devreese B, Van Beeumen J, Marita JM, Ralph J, Chen C, Burggraeve B, Van Montagu M, Messens E, Boerjan W.", TITLE = "Modifications in lignin and accumulation of phenolic glucosides in poplar xylem upon down-regulation of caffeoyl-coenzyme A O-methyltransferase, an enzyme involved in lignin biosynthesis.", JOURNAL = c("J Biol Chem 275:36899-909 (2000)", "DOI:10.1074/jbc.M006915200"\n)), list(REFERENCE = "PMID:16027976", AUTHORS = "Gachon CM, Langlois-Meurinne M, Henry Y, Saindrenan P.", TITLE = "Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications.", JOURNAL = c("Plant Mol Biol 58:229-45 (2005)", "DOI:10.1007/s11103-005-5346-5")), list(REFERENCE = "PMID:10692459", AUTHORS = "Li L, Popko JL, Umezawa T, Chiang VL.", TITLE = "5-hydroxyconiferyl aldehyde modulates enzymatic methylation for syringyl monolignol formation, a new view of monolignol biosynthesis in angiosperms.", JOURNAL = c("J Biol Chem 275:6537-45 (2000)", "DOI:10.1074/jbc.275.9.6537")), list(REFERENCE = "PMID:12009990", AUTHORS = "Yamauchi K, Yasuda S, Fukushima K.", TITLE = "Evidence for the biosynthetic pathway from sinapic acid to syringyl lignin using labeled sinapic acid with stable isotope at both methoxy groups in Robinia pseudoacacia and Nerium indicum.", JOURNAL = c("J Agric Food Chem 50:3222-7 (2002)", "DOI:10.1021/jf011565x")), list(REFERENCE = "PMID:12084820", AUTHORS = "Eckardt NA.", TITLE = "Probing the mysteries of lignin biosynthesis: the crystal structure of caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase provides new insights.", JOURNAL = c("Plant Cell 14:1185-9 (2002)", "DOI:10.1105/tpc.140610"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00940 Phenylpropanoid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

64
NODES

85
EDGES

97
ORGANISMS

11
COMMUNITIES

2.6563
AVG. DEGREE

0.0043
AVG. BETWEENNESS

12
ARTICULATION POINTS

52
OTHER NODES

Filters

Pathway Viewer

64

85

ec:2.3.1.133_1

19

11

2.6563

0.0043

12

4

13

52

97

97

0

0

97

0

0

0

0

Global metrics
Communities	Avg. degree	Avg. betweenness
11	2.6563	0.0043

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00940 Phenylpropanoid biosynthesis Metabolism; Biosynthesis of other secondary metabolites

64 NODES

85 EDGES

97 ORGANISMS

11 COMMUNITIES

2.6563 AVG. DEGREE

0.0043 AVG. BETWEENNESS

12 ARTICULATION POINTS

52 OTHER NODES