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
52	61

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.14.14.17	23

Global metrics
Communities	Avg. degree	Avg. betweenness
8	2.3462	0.0240

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
35	6	10	17

Module

Cholesterol biosynthesis, squalene 2,3-epoxide => cholesterol [PATH:map00100], Ergocalciferol biosynthesis [PATH:map00100], Cholecalciferol biosynthesis [PATH:map00100]

Lysosomal acid lipase deficiency, Smith-Lemli-Opitz syndrome, Congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD), Desmosterolosis, Vitamin D-dependent rickets, X-linked chondrodysplasia punctata, Lathosterolosis, Hypercalcemia infantile, CK syndrome, MEND syndrome

Associated organisms count

Total organisms
1085

Eukaryotes	Prokaryotes
502	583

Animals	Plants	Fungi	Protists	Bacteria	Archaea
247	105	123	27	525	58

GO associated terms

GO: 0016126

KO pathway

ko00100

References

list(REFERENCE = "", AUTHORS = "Koshiba K, Kamiya Y.", TITLE = "[Atarasii Syokubutuhorumon no Kagaku] (In Japanese)", JOURNAL = "Koudansya saientific:199-138 (2002)"), list(REFERENCE = "PMID:16531502", AUTHORS = "Morikawa T, Mizutani M, Aoki N, Watanabe B, Saga H, Saito S, Oikawa A, Suzuki H, Sakurai N, Shibata D, Wadano A, Sakata K, Ohta D.", TITLE = "Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato.", JOURNAL = c("Plant Cell 18:1008-22 (2006)", "DOI:10.1105/tpc.105.036012")), list(REFERENCE = "PMID:12777052", AUTHORS = "Lange BM, Ghassemian M.", TITLE = "Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism.", JOURNAL = c("Plant Mol Biol 51:925-48 (2003)", "DOI:10.1023/A:1023005504702"))

KPV - KEGG Pathway Viewer
by Igor Brandão

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00100 Steroid biosynthesis
Metabolism; Lipid metabolism

52
NODES

61
EDGES

1085
ORGANISMS

8
COMMUNITIES

2.3462
AVG. DEGREE

0.0240
AVG. BETWEENNESS

35
ARTICULATION POINTS

17
OTHER NODES

Filters

Pathway Viewer

52

61

ec:1.14.14.17

23

8

2.3462

0.0240

35

6

10

17

1085

502

583

247

105

123

27

525

58

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00100 Steroid biosynthesis Metabolism; Lipid metabolism

52 NODES

61 EDGES

1085 ORGANISMS

8 COMMUNITIES

2.3462 AVG. DEGREE

0.0240 AVG. BETWEENNESS

35 ARTICULATION POINTS

17 OTHER NODES