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.

00120 Primary bile acid biosynthesis
Metabolism; Lipid metabolism

Bile acids are steroid carboxylic acids derived from cholesterol in vertebrates. The primary bile acids, cholic acid and chenodeoxycholic acid, are synthesized in the liver and conjugated with taurine or glycine before secretion via bile into the intestine. The conversion from cholesterol to cholic and chenodeoxycholic acids involves four steps: 1) the initiation of synthesis by 7alpha-hydroxylation of sterol precursors, 2) further modifications to the ring structures, 3) side-chain oxidation and shortening (cleavage) by three carbons, and 4) conjugation of the bile acid with taurine or glycine.

Network metrics

Nodes	Edges
47	71

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.1.1.50_1	14

Global metrics
Communities	Avg. degree	Avg. betweenness
8	2.4444	0.0045

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
17	3	9	30

Description

Class

Metabolism; Lipid metabolism

Map

Primary bile acid biosynthesis

Module

Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate [PATH:map00120], Conjugated bile acid biosynthesis, cholate => taurocholate/glycocholate [PATH:map00120], beta-Oxidation, peroxisome, tri/dihydroxycholestanoyl-CoA => choloyl/chenodeoxycholoyl-CoA [PATH:map00120]

Associated diseases

Cerebrotendinous xanthomatosis, Peroxisomal beta-oxidation enzyme deficiency, Congenital bile acid synthesis defect, Leukoencephalopathy with dystonia and motor neuropathy, Perrault syndrome, D-bifunctional protein deficiency, Alpha-methylacyl-CoA racemase deficiency

Associated organisms count

Total organisms
145

Eukaryotes	Prokaryotes
145	0

Animals	Plants	Fungi	Protists	Bacteria	Archaea
145	0	0	0	0	0

GO associated terms

KO pathway

ko00120

References

list(REFERENCE = "PMID:12543708", AUTHORS = "Russell DW", TITLE = "The enzymes, regulation, and genetics of bile acid synthesis.", JOURNAL = c("Annu Rev Biochem 72:137-74 (2003)", "DOI:10.1146/annurev.biochem.72.121801.161712")), list(REFERENCE = "PMID:17346171", AUTHORS = "Norlin M, Wikvall K", TITLE = "Enzymes in the conversion of cholesterol into bile acids.", JOURNAL = c("Curr Mol Med 7:199-218 (2007)", "DOI:10.2174/156652407780059168")), list(REFERENCE = "PMID:10198776", AUTHORS = "Vlahcevic ZR, Pandak WM, Stravitz RT", TITLE = "Regulation of bile acid biosynthesis.", JOURNAL = c("Gastroenterol Clin North Am 28:1-25, v (1999)", "DOI:10.1016/S0889-8553(05)70041-8")), list(REFERENCE = "PMID:18081658", AUTHORS = "Pellicoro A, Faber KN", TITLE = "Review article: The function and regulation of proteins involved in bile salt biosynthesis and transport.", JOURNAL = c("Aliment Pharmacol Ther 26 Suppl 2:149-60 (2007)", "DOI:10.1111/j.1365-2036.2007.03522.x")), list(REFERENCE = "PMID:18488143", AUTHORS = "Hofmann AF, Hagey LR", TITLE = "Bile acids: chemistry, pathochemistry, biology, pathobiology, and therapeutics.", JOURNAL = c("Cell Mol Life Sci 65:2461-83 (2008)", "DOI:10.1007/s00018-008-7568-6")), list(REFERENCE = "PMID:11067870", AUTHORS = "Schwarz M, Wright AC, Davis DL, Nazer H, Bjorkhem I, Russell DW", TITLE = "The bile acid synthetic gene 3beta-hydroxy-Delta(5)-C(27)-steroid oxidoreductase is mutated in progressive intrahepatic cholestasis.", JOURNAL = c("J Clin Invest 106:1175-84 (2000)", "DOI:10.1172/JCI10902")), list(REFERENCE = "PMID:16299351", AUTHORS = "Ridlon JM, Kang DJ, Hylemon PB", TITLE = "Bile salt biotransformations by human intestinal bacteria.", JOURNAL = c("J Lipid Res 47:241-59 (2006)", "DOI:10.1194/jlr.R500013-JLR200")), list(REFERENCE = "PMID:9292932", AUTHORS = "Bortolini O, Medici A, Poli S", TITLE = "Biotransformations on steroid nucleus of bile acids.", JOURNAL = c("Steroids 62:564-77 (1997)", "DOI:10.1016/S0039-128X(97)00043-3"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00120 Primary bile acid biosynthesis
Metabolism; Lipid metabolism

47
NODES

71
EDGES

145
ORGANISMS

8
COMMUNITIES

2.4444
AVG. DEGREE

0.0045
AVG. BETWEENNESS

17
ARTICULATION POINTS

30
OTHER NODES

Filters

Pathway Viewer

47

71

ec:1.1.1.50_1

14

8

2.4444

0.0045

17

3

9

30

145

145

0

145

0

0

0

0

0

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00120 Primary bile acid biosynthesis Metabolism; Lipid metabolism

47 NODES

71 EDGES

145 ORGANISMS

8 COMMUNITIES

2.4444 AVG. DEGREE

0.0045 AVG. BETWEENNESS

17 ARTICULATION POINTS

30 OTHER NODES