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NP-KG: Knowledge Graph Framework for Natural Product-Drug Interactions
https://doi.org/10.5281/zenodo.6814507
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Graph report from 🍇 GRAPE #5

Closed LucaCappelletti94 closed 2 years ago

LucaCappelletti94 commented 2 years ago

Hello, I will leave the report for the directed graph version here. Do feel free to do what you may want with it.

I will soon post the undirected version in a comment.

NPKG

The directed multigraph NPKG has 757.83K heterogeneous nodes and 7.25M heterogeneous edges. The RAM requirements for the nodes and edges data structures are 193.02MB and 17.07MB, respectively.

Degree centrality

The minimum node degree is 0, the maximum node degree is 21.86K, the mode degree is 2, the mean degree is 9.57, and the node degree median is 3.

The nodes with the highest degree centrality are http://purl.obolibrary.org/obo/UBERON_0000473 (degree 21.86K and node type testis), http://purl.obolibrary.org/obo/GO_0005515 (degree 12.33K and node type protein binding), http://purl.obolibrary.org/obo/UBERON_0000007 (degree 10.73K and node type pituitary gland), http://purl.obolibrary.org/obo/UBERON_0002046 (degree 10.56K and node type thyroid gland) and http://purl.obolibrary.org/obo/UBERON_0001323 (degree 10.39K and node type tibial nerve).

Node types

The graph has 707.46K node types, of which the 10 most common are 3R (6.37K nodes, 0.84%), 3S (2.89K nodes, 0.38%), 4S (2.33K nodes, 0.31%), 4R (1.47K nodes, 0.19%), 9S (1.39K nodes, 0.18%), 9R (1.33K nodes, 0.18%), signal peptide removed form (human)" (1.21K nodes, 0.16%), 7R (1.15K nodes, 0.15%), 7S (1.15K nodes, 0.15%) and 2 (1.13K nodes, 0.15%). The RAM requirement for the node types data structure is 165.16MB.

Singleton node types

Singleton node types are node types that are assigned exclusively to a single node, making the node type relatively meaningless, as it adds no more information than the node name itself. The graph contains 702.25K singleton node types, which are syntaphilin isoform h1 (human) (http://purl.obolibrary.org/obo/PR_O15079-1 (degree 2 and node type syntaphilin isoform h1 (human))), ASXL2-205 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000672666 (degree 3 and node type ASXL2-205)), GNG2-205 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000554736 (degree 4 and node type GNG2-205)), alpha-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide(t18:0) (http://purl.obolibrary.org/obo/CHEBI_144633 (degree 3 and node type alpha-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide(t18:0))), Pro-Thr-Phe (http://purl.obolibrary.org/obo/CHEBI_162683 (node type Pro-Thr-Phe)), pachyonychia congenita 4 (http://purl.obolibrary.org/obo/MONDO_0014325 (degree 7 and node type pachyonychia congenita 4)), Arg-Thr-Asn (http://purl.obolibrary.org/obo/CHEBI_159322 (node type Arg-Thr-Asn)), PCDH7-208 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000621961 (degree 3 and node type PCDH7-208)), ZNF630-201 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000276054 (degree 4 and node type ZNF630-201)) and MDM2-215 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000428863 (degree 3 and node type MDM2-215)), plus other 702.24K singleton node types.

Unknown node types

Nodes with unknown node types are nodes with a node type that was not provided during the creation of the graph, which may be desired as the output of a node-label holdout. The graph contains 61 nodes with unknown node type, which are http://purl.obolibrary.org/obo/NCIT_C68749 (degree 1), http://purl.obolibrary.org/obo/PR_P69345 (degree 3), http://purl.obolibrary.org/obo/GO_0005578 (degree 1), http://purl.obolibrary.org/obo/NCBITaxon_9775 (degree 1), http://purl.obolibrary.org/obo/MFOMD_0000107 (degree 1), http://purl.obolibrary.org/obo/NCBITaxon_399537 (degree 1), http://purl.obolibrary.org/obo/NCIT_C37109 (degree 1), http://purl.obolibrary.org/obo/NCBITaxon_9261 (degree 1), http://purl.obolibrary.org/obo/MFOMD_0000101 (degree 1) and http://purl.obolibrary.org/obo/NBO_0000034 (degree 1), plus other 51 nodes with unknown node types, making up 0.01 of the nodes.

Edge types

The graph has 299 edge types, of which the 10 most common are http://www.w3.org/2000/01/rdf-schema#subClassOf (1.16M edges, 16.01%), http://purl.obolibrary.org/obo/RO_0002436 (1.01M edges, 14.00%), http://purl.obolibrary.org/obo/RO_0001025 (688.97K edges, 9.50%), http://purl.obolibrary.org/obo/RO_0001015 (688.79K edges, 9.50%), http://purl.obolibrary.org/obo/RO_0002201 (420.57K edges, 5.80%), http://purl.obolibrary.org/obo/RO_0002200 (420.57K edges, 5.80%), http://purl.obolibrary.org/obo/RO_0000057 (381.16K edges, 5.26%), http://purl.obolibrary.org/obo/RO_0000056 (381.14K edges, 5.26%), http://purl.obolibrary.org/obo/RO_0002606 (275.76K edges, 3.80%) and http://purl.obolibrary.org/obo/RO_0002302 (275.28K edges, 3.80%). The RAM requirement for the edge types data structure is 29.07MB.

Singleton edge types

Singleton edge types are edge types that are assigned exclusively to a single edge, making the edge type relatively meaningless, as it adds no more information than the name of edge itself. The graph contains 42 edges with singleton edge types, which are http://purl.obolibrary.org/obo/GO_0016579, http://purl.obolibrary.org/obo/RO_0002480, http://purl.obolibrary.org/obo/RO_0002002, http://purl.obolibrary.org/obo/RO_0003309, http://purl.obolibrary.org/obo/mondo#disease_has_basis_in_accumulation_of, http://purl.obolibrary.org/obo/uberon/core#evolved_from, http://purl.obolibrary.org/obo/RO_0002482, http://purl.obolibrary.org/obo/RO_0002497, http://purl.obolibrary.org/obo/CLO_0054408 and http://purl.obolibrary.org/obo/CLO_0054409, plus other 32 edges with singleton edge types.

Topological Oddities

A topological oddity is a set of nodes in the graph that may be derived by an error during the generation of the edge list of the graph and, depending on the task, could bias the results of topology-based models. Note that in a directed graph we only support the detection of isomorphic nodes. In the following paragraph, we will describe the detected topological oddities.

Singleton nodes

A singleton node is a node disconnected from all other nodes. We have detected 12.31K singleton nodes in the graph, involving a total of 12.31K nodes (1.62%). The detected singleton nodes are:

And other 12.30K singleton nodes.

Isomorphic node groups

Isomorphic groups are nodes with exactly the same neighbours and node types (if present in the graph). Nodes in such groups are topologically indistinguishable, that is swapping their ID would not change the graph topology. We have detected 5.98K isomorphic node groups in the graph, involving a total of 57.72K nodes (7.62%) and 756.89K edges (10.44%), with the largest one involving 8.78K nodes and 52.65K edges. The detected isomorphic node groups, sorted by decreasing size, are:

  1. Group with 8.78K nodes (degree 6 and node type DA04093 cell): http://purl.obolibrary.org/obo/CLO_0029419, http://purl.obolibrary.org/obo/CLO_0022715, http://purl.obolibrary.org/obo/CLO_0017887, http://purl.obolibrary.org/obo/CLO_0036426, http://purl.obolibrary.org/obo/CLO_0036483 and other 8.77K.

  2. Group with 758 nodes (degree 55 and node type Y_RNA.281-201): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000364774, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000363549, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000516933, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000363746, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000362807 and other 753.

  3. Group with 6.33K nodes (degree 6 and node type GM18869 cell): http://purl.obolibrary.org/obo/CLO_0026252, http://purl.obolibrary.org/obo/CLO_0020148, http://purl.obolibrary.org/obo/CLO_0010791, http://purl.obolibrary.org/obo/CLO_0026960, http://purl.obolibrary.org/obo/CLO_0010628 and other 6.33K.

  4. Group with 426 nodes (degree 56 and node type LINC00342-207): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000660608, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000667622, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000428029, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000667637, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000658836 and other 421.

  5. Group with 3.09K nodes (degree 5 and node type IGF047/78 cell): http://purl.obolibrary.org/obo/CLO_0005370, http://purl.obolibrary.org/obo/CLO_0006275, http://purl.obolibrary.org/obo/CLO_0005758, http://purl.obolibrary.org/obo/CLO_0006025, http://purl.obolibrary.org/obo/CLO_0004699 and other 3.09K.

  6. Group with 238 nodes (degree 56 and node type PCBP1-AS1-270): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000614826, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000660903, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000418564, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000415060, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000598586 and other 233.

  7. Group with 151 nodes (degree 56 and node type FRG1HP-202): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000611606, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000674524, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000507287, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000582986, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000674747 and other 146.

  8. Group with 143 nodes (degree 54 and node type SNHG14-312): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000667788, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000656463, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000580438, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000654902, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000551631 and other 138.

  9. Group with 169 nodes (degree 44 and node type Metazoa_SRP.125-201): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000578843, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000613165, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000616324, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000366402, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000615037 and other 164.

  10. Group with 1.00K nodes (degree 7 and node type ND13629 cell): http://purl.obolibrary.org/obo/CLO_0034115, http://purl.obolibrary.org/obo/CLO_0020098, http://purl.obolibrary.org/obo/CLO_0036969, http://purl.obolibrary.org/obo/CLO_0022263, http://purl.obolibrary.org/obo/CLO_0022794 and other 998.

  11. Group with 143 nodes (degree 45 and node type MIR99AHG-339): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000671058, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000659209, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000669276, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000602323, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000663516 and other 138.

  12. Group with 176 nodes (degree 34 and node type PVT1-295): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000660631, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000657356, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000656693, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000658018, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000521600 and other 171.

  13. Group with 727 nodes (degree 7 and node type ND03608 cell): http://purl.obolibrary.org/obo/CLO_0013069, http://purl.obolibrary.org/obo/CLO_0015523, http://purl.obolibrary.org/obo/CLO_0017605, http://purl.obolibrary.org/obo/CLO_0027906, http://purl.obolibrary.org/obo/CLO_0028339 and other 722.

  14. Group with 86 nodes (degree 57 and node type SNHG17-282): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000669114, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000662568, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000656320, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000660064, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000662572 and other 81.

  15. Group with 678 nodes (degree 7 and node type ND13864 cell): http://purl.obolibrary.org/obo/CLO_0034600, http://purl.obolibrary.org/obo/CLO_0029029, http://purl.obolibrary.org/obo/CLO_0031286, http://purl.obolibrary.org/obo/CLO_0034092, http://purl.obolibrary.org/obo/CLO_0031698 and other 673.

And other 5.97K isomorphic node groups.

LucaCappelletti94 commented 2 years ago

Report for the undirected version:

NPKG

The undirected multigraph NPKG has 757.83K heterogeneous nodes and 6.94M heterogeneous edges. The graph contains 12.31K connected components (of which 12.31K are disconnected nodes), with the largest one containing 745.51K nodes and the smallest one containing a single node. The RAM requirements for the nodes and edges data structures are 193.02MB and 31.08MB, respectively.

Degree centrality

The minimum node degree is 0, the maximum node degree is 190.86K, the mode degree is 3, the mean degree is 18.31 and the node degree median is 4.

The nodes with the highest degree centrality are http://purl.obolibrary.org/obo/SO_0000673 (degree 190.86K and node type transcript), http://purl.obolibrary.org/obo/SO_0001483 (degree 121.02K and node type SNV), http://purl.obolibrary.org/obo/NCBITaxon_9606 (degree 116.70K and node type Homo sapiens), http://purl.obolibrary.org/obo/SO_0001217 (degree 105.05K and node type protein_coding_gene) and http://purl.obolibrary.org/obo/UBERON_0000473 (degree 43.82K and node type testis).

Node types

The graph has 707.46K node types, of which the 10 most common are 3R (6.37K nodes, 0.84%), 3S (2.89K nodes, 0.38%), 4S (2.33K nodes, 0.31%), 4R (1.47K nodes, 0.19%), 9S (1.39K nodes, 0.18%), 9R (1.33K nodes, 0.18%), signal peptide removed form (human)" (1.21K nodes, 0.16%), 7R (1.15K nodes, 0.15%), 7S (1.15K nodes, 0.15%) and 2 (1.13K nodes, 0.15%). The RAM requirement for the node types data structure is 165.16MB.

Singleton node types

Singleton node types are node types that are assigned exclusively to a single node, making the node type relatively meaningless, as it adds no more information than the node name itself. The graph contains 702.25K singleton node types, which are IPO4-205 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000558233 (degree 4 and node type IPO4-205)), syntaphilin isoform h1 (human) (http://purl.obolibrary.org/obo/PR_O15079-1 (degree 2 and node type syntaphilin isoform h1 (human))), NM_007294.4(BRCA1):c.5156_5157del (p.Val1719fs) (https://www.ncbi.nlm.nih.gov/snp/rs80357895 (degree 3 and node type NM_007294.4(BRCA1):c.5156_5157del (p.Val1719fs))), NICR155 cell (http://purl.obolibrary.org/obo/CLO_0052362 (degree 1 and node type NICR155 cell)), aldo-keto reductase family 1 member C4 (human) (http://purl.obolibrary.org/obo/PR_P17516 (degree 195 and node type aldo-keto reductase family 1 member C4 (human))), Gonadal neoplasm (http://purl.obolibrary.org/obo/HP_0010785 (degree 9 and node type Gonadal neoplasm)), CTNNB1-210 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000453024 (degree 4 and node type CTNNB1-210)), chest bone (http://purl.obolibrary.org/obo/UBERON_0003459 (degree 4 and node type chest bone)), ASXL2-205 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000672666 (degree 4 and node type ASXL2-205)) and GNG2-205 (https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000554736 (degree 6 and node type GNG2-205)), plus other 702.24K singleton node types.

Unknown node types

Nodes with unknown node types are nodes with a node type that was not provided during the creation of the graph, which may be desired as the output of a node-label holdout. The graph contains 61 nodes with unknown node type, which are http://purl.obolibrary.org/obo/NCIT_C68749 (degree 3), http://purl.obolibrary.org/obo/PR_P69345 (degree 3), http://purl.obolibrary.org/obo/GO_0005578 (degree 2), http://purl.obolibrary.org/obo/NCBITaxon_9775 (degree 2), http://purl.obolibrary.org/obo/MFOMD_0000107 (degree 2), http://purl.obolibrary.org/obo/NCBITaxon_399537 (degree 2), http://purl.obolibrary.org/obo/NCIT_C37109 (degree 2), http://purl.obolibrary.org/obo/NCBITaxon_9261 (degree 2), http://purl.obolibrary.org/obo/MFOMD_0000101 (degree 2) and http://purl.obolibrary.org/obo/NBO_0000034 (degree 2), plus other 51 nodes with unknown node types, making up 0.01 of the nodes.

Edge types

The graph has 299 edge types, of which the 10 most common are http://www.w3.org/2000/01/rdf-schema#subClassOf (2.32M edges, 16.72%), http://purl.obolibrary.org/obo/RO_0002436 (1.41M edges, 10.17%), http://purl.obolibrary.org/obo/RO_0001025 (1.38M edges, 9.93%), http://purl.obolibrary.org/obo/RO_0001015 (1.38M edges, 9.93%), http://purl.obolibrary.org/obo/RO_0002201 (841.13K edges, 6.06%), http://purl.obolibrary.org/obo/RO_0002200 (841.13K edges, 6.06%), http://purl.obolibrary.org/obo/RO_0000057 (762.32K edges, 5.49%), http://purl.obolibrary.org/obo/RO_0000056 (762.28K edges, 5.49%), http://purl.obolibrary.org/obo/RO_0002606 (551.52K edges, 3.98%) and http://purl.obolibrary.org/obo/RO_0002302 (550.55K edges, 3.97%). The RAM requirement for the edge types data structure is 55.57MB.

Isomorphic edge types

Isomorphic edge types groups are edge types describing exactly the same set of edges. The presence of such duplicated edge types suggests a potential modelling error in the pipeline that has produced this graph. 6 isomorphic edge types groups were detected in this graph. We currently compute and display the isomorphic edge types with at least 20 edges.

  1. Isomorphic edge type group containing 2 edge types (841.13K edges, 6.06%), which are: http://purl.obolibrary.org/obo/RO_0002200 and http://purl.obolibrary.org/obo/RO_0002201.

  2. Isomorphic edge type group containing 2 edge types (365.43K edges, 2.63%), which are: http://purl.obolibrary.org/obo/RO_0002510 and http://purl.obolibrary.org/obo/RO_0002511.

  3. Isomorphic edge type group containing 2 edge types (145.02K edges, 1.05%), which are: http://purl.obolibrary.org/obo/RO_0000085 and http://purl.obolibrary.org/obo/RO_0000079.

  4. Isomorphic edge type group containing 2 edge types (88.40K edges, 0.64%), which are: http://purl.obolibrary.org/obo/RO_0002513 and http://purl.obolibrary.org/obo/RO_0002512.

  5. Isomorphic edge type group containing 2 edge types (39.05K edges, 0.28%), which are: http://purl.obolibrary.org/obo/RO_0002204 and http://purl.obolibrary.org/obo/RO_0002205.

  6. Isomorphic edge type group containing 2 edge types (16.04K edges, 0.12%), which are: http://purl.obolibrary.org/obo/chebi#is_conjugate_acid_of and http://purl.obolibrary.org/obo/chebi#is_conjugate_base_of.

Singleton edge types

Singleton edge types are edge types that are assigned exclusively to a single edge, making the edge type relatively meaningless, as it adds no more information than the name of edge itself. The graph contains 6 edges with singleton edge types, which are http://purl.obolibrary.org/obo/RO_0002482, http://purl.obolibrary.org/obo/RO_0002481, http://purl.obolibrary.org/obo/RO_0002465, http://purl.obolibrary.org/obo/RO_0002466, http://purl.obolibrary.org/obo/RO_0002467 and http://purl.obolibrary.org/obo/RO_0002468.

Topological Oddities

A topological oddity is a set of nodes in the graph that may be derived by an error during the generation of the edge list of the graph and, depending on the task, could bias the results of topology-based models. In the following paragraph, we will describe the detected topological oddities.

Singleton nodes

A singleton node is a node disconnected from all other nodes. We have detected 12.31K singleton nodes in the graph, involving a total of 12.31K nodes (1.62%). The detected singleton nodes are:

And other 12.30K singleton nodes.

Chains

A chain is a path of nodes with unique degree 2, that is ignoring self-loop and multi-edges, connecting two strongly connected components of the graph. We have detected a single chain in the graph, involving a total of 10 nodes and 9 edges, with the largest one involving 10 nodes and 9 edges.

Isomorphic node groups

Isomorphic groups are nodes with exactly the same neighbours and node types (if present in the graph). Nodes in such groups are topologically indistinguishable, that is swapping their ID would not change the graph topology. We have detected 17.11K isomorphic node groups in the graph, involving a total of 97.38K nodes (12.85%) and 1.46M edges (10.53%), with the largest one involving 8.78K nodes and 81.86K edges. The detected isomorphic node groups, sorted by decreasing size, are:

  1. Group with 758 nodes (degree 108 and node type Y_RNA.607-201): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000410597, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000516306, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000363428, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000618679, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000364908 and other 753.

  2. Group with 8.78K nodes (degree 6 and node type ND08676 cell): http://purl.obolibrary.org/obo/CLO_0014019, http://purl.obolibrary.org/obo/CLO_0010592, http://purl.obolibrary.org/obo/CLO_0030840, http://purl.obolibrary.org/obo/CLO_0023612, http://purl.obolibrary.org/obo/CLO_0013643 and other 8.77K.

  3. Group with 426 nodes (degree 110 and node type SNHG5-226): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000655116, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000668680, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000661984, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000519454, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000542265 and other 421.

  4. Group with 6.33K nodes (degree 6 and node type DA02927 cell): http://purl.obolibrary.org/obo/CLO_0013926, http://purl.obolibrary.org/obo/CLO_0036869, http://purl.obolibrary.org/obo/CLO_0020316, http://purl.obolibrary.org/obo/CLO_0023222, http://purl.obolibrary.org/obo/CLO_0026140 and other 6.33K.

  5. Group with 238 nodes (degree 110 and node type PCBP1-AS1-380): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000654878, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000629178, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000655140, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000661703, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000629605 and other 233.

  6. Group with 151 nodes (degree 110 and node type TUG1-205): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000566220, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000456312, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000649495, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000551681, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000674747 and other 146.

  7. Group with 3.09K nodes (degree 5 and node type IGF046/98 cell): http://purl.obolibrary.org/obo/CLO_0005367, http://purl.obolibrary.org/obo/CLO_0008539, http://purl.obolibrary.org/obo/CLO_0005749, http://purl.obolibrary.org/obo/CLO_0005189, http://purl.obolibrary.org/obo/CLO_0005266 and other 3.09K.

  8. Group with 143 nodes (degree 106 and node type SNHG14-288): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000663945, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000663359, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000657237, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000658623, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000669928 and other 138.

  9. Group with 169 nodes (degree 86 and node type Metazoa_SRP.101-201): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000610878, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000622203, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000613350, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000618435, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000547793 and other 164.

  10. Group with 143 nodes (degree 88 and node type MIR99AHG-270): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000660794, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000667703, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000653809, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000435697, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000666517 and other 138.

  11. Group with 176 nodes (degree 66 and node type PVT1-213): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000522414, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000664214, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000667149, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000657112, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000658158 and other 171.

  12. Group with 86 nodes (degree 112 and node type SNHG17-238): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000659102, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000658455, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000669137, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000413755, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000664073 and other 81.

  13. Group with 89 nodes (degree 104 and node type MIR100HG-255): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000657990, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000660603, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000663802, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000648209, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000666347 and other 84.

  14. Group with 107 nodes (degree 84 and node type MIR4435-2HG-255): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000664999, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000622940, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000666652, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000643766, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000673843 and other 102.

  15. Group with 72 nodes (degree 112 and node type FTX-249): https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000659407, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000661084, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000668224, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000661335, https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000651703 and other 67.

And other 17.09K isomorphic node groups.

Dendritic trees

A dendritic tree is a tree-like structure starting from a root node that is part of another strongly connected component. We have detected 714 dendritic trees in the graph, involving a total of 15.79K nodes (2.08%) and 31.57K edges (0.23%), with the largest one involving 2.51K nodes and 5.03K edges. The detected dendritic trees, sorted by decreasing size, are:

  1. Dendritic tree starting from the root node http://purl.obolibrary.org/obo/CLO_0000019 (degree 2.61K and node type immortal cell line cell), and containing 2.51K nodes, with a maximal depth of 3, which are http://purl.obolibrary.org/obo/CLO_0008131 (node type NCTC 2071 cell), http://purl.obolibrary.org/obo/CLO_0003715 (node type Hermes-3 cell), http://purl.obolibrary.org/obo/CLO_0003960 (node type Hs 431 cell), http://purl.obolibrary.org/obo/CLO_0052902 (node type NICR365 cell) and http://purl.obolibrary.org/obo/CLO_0007504 (node type mAb 13-1 cell). Its nodes have 2.50K node types, of which the 10 most common are 10 (3 nodes), Sp2/0-Ag14 cell (2 nodes), L368 cell (2 nodes), H25B10 cell (2 nodes), DS-1 cell (2 nodes), 15C6 cell (2 nodes), OKT 5 cell (2 nodes), Hybridoma 234 s.2a cell (2 nodes), SC-1 cell (2 nodes) and P3X63Ag8.653 derived cell line cell (2 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  2. Dendritic tree starting from the root node http://purl.obolibrary.org/obo/CHEBI_50860 (degree 2.70K and node type organic molecular entity), and containing 1.32K nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/CHEBI_80156 (node type Endomorphin-1), http://purl.obolibrary.org/obo/CHEBI_143609 (node type Cer(d16:0(15Me)/23:0)), http://purl.obolibrary.org/obo/CHEBI_144080 (node type 2-acyl-sn-glycero-3-phospho)-1D-myo-2-acyl-inositol zwitterion"), http://purl.obolibrary.org/obo/CHEBI_1480 (node type 3-Decanoyl-[acyl-carrier protein]) and http://purl.obolibrary.org/obo/CHEBI_139680 (node type ascr#30-CoA(4-)). Its nodes have 1.29K node types, of which the 10 most common are 5 (21 nodes), 9 (9 nodes), 2-acyl-sn-glycero-3-phospho)-1D-myo-2-acyl-inositol zwitterion" (4 nodes), N (2 nodes), Asp (2 nodes), bkos#38(1-), Lumirhodopsin, Flopropione, Arylhydroxamate and Magnesium L-ascorbic acid-2-phosphate. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  3. Dendritic tree starting from the root node http://purl.obolibrary.org/obo/CHEBI_25477 (degree 601 and node type naphthalenes), and containing 412 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/CHEBI_124720 (node type 3R)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-10-[[(1-naphthalenylamino)-oxomethyl]amino]-6-oxo-3), http://purl.obolibrary.org/obo/CHEBI_108992 (node type 4-(2-naphthalenyloxymethyl)-2-thiazolamine), http://purl.obolibrary.org/obo/CHEBI_115726 (node type 4-diene-1-carboxamide"), http://purl.obolibrary.org/obo/CHEBI_34108 (node type 1-Nitrosonaphthalene) and http://purl.obolibrary.org/obo/CHEBI_127380 (node type 3R)-2-[[cyclohexylmethyl(methyl)amino]methyl]-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-6-oxo-2). Its nodes have 265 node types, of which the 10 most common are 3 (32 nodes), 3R)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[(1-naphthalenylamino)-oxomethyl]amino]methyl]-6-oxo-3 (8 nodes), 3S)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[(1-naphthalenylamino)-oxomethyl]amino]methyl]-6-oxo-3 (8 nodes), 4 (7 nodes), 3R)-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[(1-naphthalenylamino)-oxomethyl]amino]methyl]-6-oxo-3 (6 nodes), 3S)-2-[[1 (6 nodes), 3S)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-10-[[(1-naphthalenylamino)-oxomethyl]amino]-6-oxo-3 (5 nodes), 3S)-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[(1-naphthalenylamino)-oxomethyl]amino]methyl]-6-oxo-3 (5 nodes), 3R)-2-[[1 (5 nodes) and 3R)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-10-[[(1-naphthalenylamino)-oxomethyl]amino]-6-oxo-3 (5 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  4. Dendritic tree starting from the root node http://purl.obolibrary.org/obo/CHEBI_24828 (degree 596 and node type indoles), and containing 343 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/CHEBI_125378 (node type N-[(4-chlorophenyl)-(2-methyl-1H-indol-3-yl)methyl]-2-pyridinamine), http://purl.obolibrary.org/obo/CHEBI_109271 (node type 4-dihydro-2H-carbazol-1-yl)hydrazine"), http://purl.obolibrary.org/obo/CHEBI_114853 (node type [1-[2-(2-methylphenoxy)ethyl]-3-indolyl]-(4-methyl-1-piperazinyl)methanethione), http://purl.obolibrary.org/obo/CHEBI_121239 (node type LSM-32682) and http://purl.obolibrary.org/obo/CHEBI_108553 (node type [[1-[(4-fluorophenyl)methyl]-2-oxo-3-indolylidene]amino]thiourea). Its nodes have 284 node types, of which the 10 most common are 3 (12 nodes), 2 (11 nodes), 3'R (5 nodes), 5 (5 nodes), 3R)-2-[[1 (4 nodes), 3-dihydroindole-5-sulfonamide" (4 nodes), 3S)-2-[[1 (4 nodes), 3'S (3 nodes), 3S)-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl(pyridin-4-ylmethyl)amino]methyl]-6-oxo-3 (2 nodes) and 3-dione" (2 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  5. Dendritic tree starting from the root node http://purl.obolibrary.org/obo/CHEBI_57643 (degree 520 and node type 2-diacyl-sn-glycero-3-phosphocholine"), and containing 309 nodes, with a maximal depth of 4, which are http://purl.obolibrary.org/obo/CHEBI_89441 (node type 12Z), http://purl.obolibrary.org/obo/CHEBI_89512 (node type 11Z), http://purl.obolibrary.org/obo/CHEBI_34119 (node type 1-Palmitoyl-2-(5-hydroxy-8-oxo-6-octenedioyl)-sn-glycero-3-phosphatidylcholine), http://purl.obolibrary.org/obo/CHEBI_89431 (node type 9Z) and http://purl.obolibrary.org/obo/CHEBI_89294 (node type 11Z). Its nodes have 154 node types, of which the 10 most common are 9Z (36 nodes), 8Z (32 nodes), 11Z (32 nodes), 12Z (20 nodes), 10Z (17 nodes), 7Z (10 nodes), 14Z))" (7 nodes), 12Z))" (5 nodes), 16Z))" (5 nodes) and phosphatidylcholine 41:3. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  6. Dendritic tree starting from the root node http://purl.obolibrary.org/obo/CLO_0000001 (degree 11 and node type cell line cell), and containing 283 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/CLO_0000018 (degree 281 and node type mortal cell line cell), http://purl.obolibrary.org/obo/CLO_0000026 (node type suspension cell line cell), http://purl.obolibrary.org/obo/CLO_0000027 (node type adherent cell line cell), http://purl.obolibrary.org/obo/CLO_0053217 (node type NICR1397 cell) and http://purl.obolibrary.org/obo/CLO_0052844 (node type NICR1363 cell). Its nodes have 283 node types, of which the 10 most common are NICR1283 cell, NICR2221 cell, NICR2247 cell, NICR872 cell, NICR2078 cell, NICR1356 cell, NICR1632 cell, NICR1390 cell, NICR1289 cell and NICR149 cell. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

And other 708 dendritic trees.

Dendritic stars

A dendritic star is a dendritic tree with a maximal depth of one, where nodes with maximal unique degree one are connected to a central root node with high degree and inside a strongly connected component. We have detected 3.98K dendritic stars in the graph, involving a total of 54.76K nodes (7.23%) and 109.52K edges (0.79%), with the largest one involving 2.52K nodes and 5.04K edges. The detected dendritic stars, sorted by decreasing size, are:

  1. Dendritic star starting from the root node http://purl.obolibrary.org/obo/CHEBI_35358 (degree 3.92K and node type sulfonamide), and containing 2.52K nodes, with a maximal depth of 1, which are http://purl.obolibrary.org/obo/CHEBI_113965 (node type 3S)-8-bromo-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-6-oxo-3), http://purl.obolibrary.org/obo/CHEBI_128463 (node type 3R)-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-(phenylmethyl)amino]methyl]-6-oxo-3), http://purl.obolibrary.org/obo/CHEBI_108159 (node type N-[3-[methyl(methylsulfonyl)amino]phenyl]-2-phenoxyacetamide), http://purl.obolibrary.org/obo/CHEBI_103672 (node type 5R)-8-(1-cyclopentenyl)-2-[(2R)-1-hydroxypropan-2-yl]-4-methyl-1) and http://purl.obolibrary.org/obo/CHEBI_117405 (node type 3R). Its nodes have 974 node types, of which the 10 most common are 3R (257 nodes, 0.03%), 3S (250 nodes, 0.03%), 4aR (71 nodes), 4aS (70 nodes), 6aS (47 nodes), 6aR (45 nodes), 3 (36 nodes), 3S)-2-[[(3 (27 nodes), 3R)-2-[[(3 (23 nodes) and 3-dihydro-1 (20 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  2. Dendritic star starting from the root node http://purl.obolibrary.org/obo/CHEBI_28963 (degree 2.42K and node type amino sugar), and containing 2.07K nodes, with a maximal depth of 1, which are http://purl.obolibrary.org/obo/CHEBI_146787 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_154559 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_153638 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_152843 (node type 4R) and http://purl.obolibrary.org/obo/CHEBI_154188 (node type 3R). Its nodes have 103 node types, of which the 10 most common are 3R (1.19K nodes, 0.16%), 4R (741 nodes, 0.10%), 3S (25 nodes), 4S (11 nodes), Istamycin AO, CID 91845806, Istamycin AP, Fortimicin FU-10, alpha-D-Glcp-(1->4)-D-GlcpNAc and GalGlcNAc2Man3GlcNAcFucGlcNAc-II. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  3. Dendritic star starting from the root node http://purl.obolibrary.org/obo/CHEBI_20857 (degree 1.96K and node type C-glycosyl compound), and containing 1.85K nodes, with a maximal depth of 1, which are http://purl.obolibrary.org/obo/CHEBI_122297 (node type 5S), http://purl.obolibrary.org/obo/CHEBI_122299 (node type 5R), http://purl.obolibrary.org/obo/CHEBI_101371 (node type 5R), http://purl.obolibrary.org/obo/CHEBI_118364 (node type 3R) and http://purl.obolibrary.org/obo/CHEBI_120079 (node type 3R). Its nodes have 32 node types, of which the 10 most common are 3R (540 nodes, 0.07%), 3S (528 nodes, 0.07%), 5R (320 nodes, 0.04%), 5S (316 nodes, 0.04%), 5-dichloro-N-[2-[(2R (12 nodes), 5-dichloro-N-[2-[(2S (12 nodes), 3-benzodioxol-5-ylmethyl)-2-[(2S (10 nodes), 3-benzodioxol-5-ylmethyl)-2-[(2R (10 nodes), 4-dichlorophenyl)methyl]-2-[(2S (9 nodes) and 4-dichlorophenyl)methyl]-2-[(2R (9 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  4. Dendritic star starting from the root node http://purl.obolibrary.org/obo/CHEBI_18154 (degree 2.88K and node type polysaccharide), and containing 1.64K nodes, with a maximal depth of 1, which are http://purl.obolibrary.org/obo/CHEBI_155808 (node type CID 91860434), http://purl.obolibrary.org/obo/CHEBI_150055 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_154254 (node type CID 91856856), http://purl.obolibrary.org/obo/CHEBI_155360 (node type 4S) and http://purl.obolibrary.org/obo/CHEBI_154270 (node type CID 91861727). Its nodes have 791 node types, of which the 10 most common are 4S (318 nodes, 0.04%), 3R (273 nodes, 0.04%), 4R (265 nodes, 0.03%), CID 91853067, CID 91859811, CID 91862762, CID 91852877, CID 91853844, beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->2)-alpha-D-Manp-(1->3)-[beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->4)]-[beta-D-Galp-(1->4)-beta-D-GlcpNAc-(1->2)-alpha-D-Manp-(1->6)]-beta-D-Manp-(1->4)-beta-D-GlcpNAc-(1->4)-[alpha-L-Fucp-(1->6)]-D-GlcpNAc and CID 91860485. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  5. Dendritic star starting from the root node http://purl.obolibrary.org/obo/CHEBI_35618 (degree 2.62K and node type aromatic ether), and containing 1.56K nodes, with a maximal depth of 1, which are http://purl.obolibrary.org/obo/CHEBI_110060 (node type 3S)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-6-oxo-8-(5-pyrimidinyl)-3), http://purl.obolibrary.org/obo/CHEBI_95879 (node type 5S)-8-(3-hydroxy-3-methylbut-1-ynyl)-2-[(2S)-1-hydroxypropan-2-yl]-4-methyl-1), http://purl.obolibrary.org/obo/CHEBI_93021 (node type 3), http://purl.obolibrary.org/obo/CHEBI_95587 (node type 9R)-6-[(2S)-1-hydroxypropan-2-yl]-8-methyl-9-[[methyl-[(4-phenoxyphenyl)methyl]amino]methyl]-10-oxa-1) and http://purl.obolibrary.org/obo/CHEBI_96296 (node type 5R)-8-[3-(dimethylamino)prop-1-ynyl]-2-[(2R)-1-hydroxypropan-2-yl]-4-methyl-1). Its nodes have 720 node types, of which the 10 most common are 2 (33 nodes), 3R (33 nodes), 3S (29 nodes), 3 (27 nodes), 4aR (18 nodes), 6aS (16 nodes), 6aR (14 nodes), 5-dimethyl-4-isoxazolyl)-3-[(2R (13 nodes), 3R)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[(4-phenoxyphenyl)methyl]amino]methyl]-6-oxo-3 (13 nodes) and 3R)-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[(4-phenoxyphenyl)methyl]amino]methyl]-6-oxo-3 (13 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  6. Dendritic star starting from the root node http://purl.obolibrary.org/obo/CHEBI_47857 (degree 1.69K and node type ureas), and containing 1.54K nodes, with a maximal depth of 1, which are http://purl.obolibrary.org/obo/CHEBI_102688 (node type 6aR), http://purl.obolibrary.org/obo/CHEBI_110408 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_99777 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_126198 (node type 3S)-8-(dimethylamino)-5-[(2S)-1-hydroxypropan-2-yl]-3-methyl-6-oxo-3) and http://purl.obolibrary.org/obo/CHEBI_98959 (node type LSM-10338). Its nodes have 503 node types, of which the 10 most common are 3R (237 nodes, 0.03%), 3S (231 nodes, 0.03%), 6aR (41 nodes), 6aS (38 nodes), 4aS (35 nodes), 4aR (32 nodes), 4 (11 nodes), 3S)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[oxo-[4-(trifluoromethyl)anilino]methyl]amino]methyl]-6-oxo-3 (10 nodes), 3R)-5-[(2R)-1-hydroxypropan-2-yl]-3-methyl-2-[[methyl-[oxo-[4-(trifluoromethyl)anilino]methyl]amino]methyl]-6-oxo-3 (10 nodes) and 3R)-4-[(2 (8 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

And other 3.98K dendritic stars.

Dendritic tendril stars

A dendritic tendril star is a dendritic tree with a depth greater than one, where the arms of the star are tendrils. We have detected 175 dendritic tendril stars in the graph, involving a total of 3.87K nodes (0.51%) and 7.74K edges (0.06%), with the largest one involving 1.80K nodes and 3.59K edges. The detected dendritic tendril stars, sorted by decreasing size, are:

  1. Dendritic tendril star starting from the root node http://purl.obolibrary.org/obo/CHEBI_50699 (degree 2.08K and node type oligosaccharide), and containing 1.80K nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/CHEBI_153201 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_148565 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_151916 (node type 3R), http://purl.obolibrary.org/obo/CHEBI_153142 (node type 4S) and http://purl.obolibrary.org/obo/CHEBI_154994 (node type 4S). Its nodes have 79 node types, of which the 10 most common are 3R (1.39K nodes, 0.18%), 3S (173 nodes, 0.02%), 4S (153 nodes, 0.02%), 4R (11 nodes), Magnoloside C, Sialyllacto-N-tetraose a, Lacto-N-fucopentaose V, Mithramycin DK, alpha-D-GalpNAc-(1->3)-beta-D-Galp-(1->3)-D-Glcp and Zizybeoside II. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  2. Dendritic tendril star starting from the root node http://purl.obolibrary.org/obo/CHEBI_22715 (degree 351 and node type benzimidazoles), and containing 266 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/CHEBI_94388 (node type 2-(2-methyl-2-pyrrolidinyl)-1H-benzimidazole-4-carboxamide), http://purl.obolibrary.org/obo/CHEBI_114308 (node type 2-(2-chloro-3-pyridinyl)-1-prop-2-enylbenzimidazole), http://purl.obolibrary.org/obo/CHEBI_91459 (node type 6-dimethoxy-1-benzimidazolyl)-3-[(2-methylsulfonylphenyl)methoxy]-2-thiophenecarbonitrile"), http://purl.obolibrary.org/obo/CHEBI_109461 (node type 2-dihydropyrazol-3-ylidene]-1-cyclohexa-2) and http://purl.obolibrary.org/obo/CHEBI_120925 (node type 2-diamine"). Its nodes have 244 node types, of which the 10 most common are 2 (7 nodes), 3 (5 nodes), 2-a]benzimidazolecarbonitrile" (5 nodes), 4 (3 nodes), 4-dihydro-1H-[1 (2 nodes), N (2 nodes), 5-dinitrobenzamide" (2 nodes), 5 (2 nodes), 3-dihydrobenzimidazol-2-one" (2 nodes) and 8 (2 nodes). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  3. Dendritic tendril star starting from the root node http://purl.obolibrary.org/obo/MONDO_0002254 (degree 706 and node type syndromic disease), and containing 230 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/MONDO_0023002 (node type double discordia), http://purl.obolibrary.org/obo/MONDO_0023052 (node type ectrodactyly polydactyly), http://purl.obolibrary.org/obo/MONDO_0004771 (node type Fuchs' heterochromic uveitis), http://purl.obolibrary.org/obo/MONDO_0022977 (node type diaphragmatic hernia exomphalos corpus callosum agenesis) and http://purl.obolibrary.org/obo/MONDO_0100071 (node type cardiocutaneous syndrome). Its nodes have 230 node types, of which the 10 most common are congenital unilateral pulmonary hypoplasia, cardiocutaneous syndrome, AIDS dysmorphic syndrome, epiphyseal dysplasia dysmorphism camptodactyly, craniofrontonasal syndrome Teebi type, gigantism advanced bone age hoarse cry, cleft palate colobomata radial synostosis deafness, dysostosis acral with facial and genital abnormalities, chronic demyelinizing neuropathy with IgM monoclonal and fenton Wilkinson Toselano syndrome. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  4. Dendritic tendril star starting from the root node http://purl.obolibrary.org/obo/GO_0016836 (degree 200 and node type hydro-lyase activity), and containing 116 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/GO_0003861 (node type 3-isopropylmalate dehydratase activity), http://purl.obolibrary.org/obo/GO_0018816 (node type 2-hydroxyisobutyrate dehydratase activity), http://purl.obolibrary.org/obo/GO_0008684 (node type 2-oxopent-4-enoate hydratase activity), http://purl.obolibrary.org/obo/GO_0008867 (node type galactarate dehydratase activity) and http://purl.obolibrary.org/obo/GO_0050215 (node type propanediol dehydratase activity). Its nodes have 115 node types, of which the 10 most common are 6-dehydratase activity" (2 nodes), galactarate dehydratase activity, trans-feruloyl-CoA hydratase activity, cyclohexyl-isocyanide hydratase activity, 3-methyl-5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridon hydratase-aldolase activity, nitrile hydratase activity, D-fuconate dehydratase activity, OPC6-trans-2-enoyl-CoA hydratase activity, naphthyl-2-methylene-succinyl-CoA lyase activity and cyclohex-1-ene-1-carboxyl-CoA hydratase activity. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  5. Dendritic tendril star starting from the root node http://purl.obolibrary.org/obo/GO_0008168 (degree 246 and node type methyltransferase activity), and containing 115 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/GO_0102918 (node type (R)-reticuline 7-O-methyltransferase activity), http://purl.obolibrary.org/obo/GO_0102450 (node type kaempferide 7-O-methyltransferase activity), http://purl.obolibrary.org/obo/GO_0102400 (node type 3), http://purl.obolibrary.org/obo/GO_0102302 (node type mycinamicin VI 2''-O-methyltransferase activity) and http://purl.obolibrary.org/obo/GO_0102432 (node type quercetin 7-O-methyltransferase activity). Its nodes have 112 node types, of which the 10 most common are 3 (3 nodes), 4' (2 nodes), norbixin methyltransferase activity, laricitrin 4'-O-methyltransferase activity, S-adenosyl-L-methionine:eugenol-O-methyltransferase activity, C4-demethylase activity, dimethyl selenide methyltransferase activity, [methyl-Co(III) methanol-specific corrinoid protein]:coenzyme M methyltransferase activity, quercetin 3'-O-methyltransferase activity and 4-hydroxytryptamine 4-phosphate methyltransferase activity. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  6. Dendritic tendril star starting from the root node http://purl.obolibrary.org/obo/GO_0016628 (degree 137 and node type acting on the CH-CH group of donors), and containing 106 nodes, with a maximal depth of 2, which are http://purl.obolibrary.org/obo/GO_0102745 (node type dihydrogeranylgeranyl-PP reductase activity), http://purl.obolibrary.org/obo/GO_0047791 (node type cucurbitacin delta23-reductase activity), http://purl.obolibrary.org/obo/GO_0050184 (node type phosphatidylcholine desaturase activity), http://purl.obolibrary.org/obo/GO_0018515 (node type pimeloyl-CoA dehydrogenase activity) and http://purl.obolibrary.org/obo/GO_0033731 (node type arogenate dehydrogenase [NAD(P)+] activity). Its nodes have 104 node types, of which the 10 most common are 3-dihydroxy-2 (2 nodes), NADPH:steroid 5alpha-reductase activity" (2 nodes), dibenzothiophene dihydrodiol dehydrogenase activity, 3-methyleneoxindole reductase activity, 4-dichlorobenzoyl-CoA reductase activity", phloroglucinol reductase activity, trans-arachidon-2-enoyl-CoA reductase activity, protochlorophyllide reductase activity, 10R-dihydrodiolphenanthrene dehydrogenase activity" and 4-cis-dihydrodiol dehydrogenase activity". Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

And other 169 dendritic tendril stars.

Tendrils

A tendril is a path starting from a node of degree one, connected to a strongly connected component. We have detected 5.98K tendrils in the graph, involving a total of 6.21K nodes (0.82%) and 12.41K edges (0.09%), with the largest one involving 8 nodes and 16 edges. The detected tendrils, sorted by decreasing size, are:

  1. Tendril starting from the root node http://purl.obolibrary.org/obo/NCBITaxon_123368 (degree 4 and node type Acanthomorphata), and containing 8 nodes, with a maximal depth of 8, which are http://purl.obolibrary.org/obo/NCBITaxon_1489838 (node type Paracanthopterygii), http://purl.obolibrary.org/obo/NCBITaxon_1489841 (node type Zeiogadaria), http://purl.obolibrary.org/obo/NCBITaxon_1489843 (node type Gadariae), http://purl.obolibrary.org/obo/NCBITaxon_8043 (node type Gadiformes) and http://purl.obolibrary.org/obo/NCBITaxon_1489845 (node type Gadoidei). Its nodes have 8 node types, which are Gadiformes, Gadus, Gadus morhua, Zeiogadaria, Gadariae, Paracanthopterygii, Gadoidei and Gadidae. Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  2. Tendril starting from the root node http://purl.obolibrary.org/obo/NCBITaxon_6236 (degree 6 and node type Rhabditida), and containing 7 nodes, with a maximal depth of 7, which are http://purl.obolibrary.org/obo/NCBITaxon_2301116 (degree 3 and node type Rhabditina), http://purl.obolibrary.org/obo/NCBITaxon_2301119 (degree 3 and node type Rhabditomorpha), http://purl.obolibrary.org/obo/NCBITaxon_55879 (degree 3 and node type Rhabditoidea), http://purl.obolibrary.org/obo/NCBITaxon_6243 (degree 3 and node type Rhabditidae) and http://purl.obolibrary.org/obo/NCBITaxon_55885 (degree 3 and node type Peloderinae). Its nodes have 7 node types, which are Rhabditina, Rhabditidae, Caenorhabditis, Rhabditomorpha, Caenorhabditis elegans, Peloderinae and Rhabditoidea. Its edges have 2 edge types, which are http://www.w3.org/2000/01/rdf-schema#subClassOf (13 edges, 65.00%) and http://purl.obolibrary.org/obo/RO_0002162 (7 edges, 35.00%).

  3. Tendril starting from the root node http://purl.obolibrary.org/obo/NCBITaxon_6448 (degree 8 and node type Gastropoda), and containing 7 nodes, with a maximal depth of 7, which are http://purl.obolibrary.org/obo/NCBITaxon_216275 (node type Vetigastropoda), http://purl.obolibrary.org/obo/NCBITaxon_2315720 (node type Trochida), http://purl.obolibrary.org/obo/NCBITaxon_216285 (node type Trochoidea ), http://purl.obolibrary.org/obo/NCBITaxon_63671 (node type Turbinidae) and http://purl.obolibrary.org/obo/NCBITaxon_63672 (node type Turbo ). Its nodes have 7 node types, which are Turbo , Batillus, Vetigastropoda, Turbinidae, Trochida, Turbo cornutus and Trochoidea . Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  4. Tendril starting from the root node http://purl.obolibrary.org/obo/NCBITaxon_1963758 (degree 4 and node type Myomorpha), and containing 5 nodes, with a maximal depth of 5, which are http://purl.obolibrary.org/obo/NCBITaxon_1963761 (degree 3 and node type Dipodoidea), http://purl.obolibrary.org/obo/NCBITaxon_30648 (degree 3 and node type Dipodidae), http://purl.obolibrary.org/obo/NCBITaxon_35737 (degree 3 and node type Dipodinae), http://purl.obolibrary.org/obo/NCBITaxon_48867 (degree 3 and node type Jaculus) and http://purl.obolibrary.org/obo/NCBITaxon_51337 (node type Jaculus jaculus). Its nodes have 5 node types, which are Dipodidae, Dipodinae, Dipodoidea, Jaculus and Jaculus jaculus. Its edges have 2 edge types, which are http://www.w3.org/2000/01/rdf-schema#subClassOf (9 edges, 64.29%) and http://purl.obolibrary.org/obo/RO_0002162 (5 edges, 35.71%).

  5. Tendril starting from the root node http://purl.obolibrary.org/obo/PO_0009011 (degree 16 and node type plant structure), and containing 5 nodes, with a maximal depth of 5, which are http://purl.obolibrary.org/obo/FOODON_03420148 (node type stem), http://purl.obolibrary.org/obo/FOODON_03420144 (node type excluding fruit and seed"), http://purl.obolibrary.org/obo/FOODON_03420237 (node type floret or flower), http://purl.obolibrary.org/obo/FOODON_03420310 (node type stamen) and http://purl.obolibrary.org/obo/FOODON_03420279 (node type pollen). Its nodes have 5 node types, which are floret or flower, stamen, stem, pollen and excluding fruit and seed". Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

  6. Tendril starting from the root node http://purl.obolibrary.org/obo/FOODON_03400361 (degree 4 and node type food product type), and containing 5 nodes, with a maximal depth of 5, which are http://purl.obolibrary.org/obo/FOODON_03400352 (node type international agency food product type), http://purl.obolibrary.org/obo/FOODON_03400643 (node type Codex Alimentarius classification of food and feed commodities), http://purl.obolibrary.org/obo/FOODON_03400644 (node type a. primary food commodities of plant origin (ccpr)), http://purl.obolibrary.org/obo/FOODON_03400652 (node type 04 nuts and seeds (ccpr)) and http://purl.obolibrary.org/obo/FOODON_03400685 (node type 022 tree nuts (tn) (ccpr)). Its nodes have 5 node types, which are 022 tree nuts (tn) (ccpr), international agency food product type, a. primary food commodities of plant origin (ccpr), Codex Alimentarius classification of food and feed commodities and 04 nuts and seeds (ccpr). Its edges have a single edge type, which is http://www.w3.org/2000/01/rdf-schema#subClassOf.

And other 5.98K tendrils.