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charles.hoyt@scai.fraunhofer.de at 2018-03-30 18:27:32
Authors
Selventa
Contact
support@belframework.org
Description
Example of modeling a full abstract taken from the BEL V1.0 Language Overview.
License
Creative Commons Attribution-Non-Commercial-ShareAlike 3.0 Unported License
Copyright
Copyright (c) 2011-2015, Selventa. All Rights Reserved.
Number Nodes
22
Number Edges
26
Number Components
1
Network Density
0.0562771
Average Degree
1.18182
Number Citations
1
Number BEL Errors
0

Content Statistics

Network Overlap

The node-based overlap between this network and other networks is calculated as the Szymkiewicz-Simpson coefficient of their respective nodes. Up to the top 10 are shown below.

Network Overlap
BEL Framework Large Corpus Document v20170611 82%
BEL Framework Small Corpus Document v20150611 55%
Colorectal Cancer Model v2.0.6 45%
CRC_combined v1.1 41%
Growth Factor-2.0-Hs v2.0 36%
Endothelial Innate Immune Activation-2.0-Mm v2.0 32%
Growth Factor-2.0-Mm v2.0 32%
Selventa Protein Families Definitions v20150611 27%
Cell Cycle-2.0-Hs v2.0 27%
Neutrophil Signaling-2.0-Mm v2.0 27%

Sample Edges

p(HGNC:KRAS, var(p.Gly12Val)) directlyIncreases complex(p(HGNC:KRAS), p(MGI:Raf1))

A molecular analysis of the induced tumors shows that the K12V mutant protein interacts with Raf-1 and transduces signals mainly through the Erk pathway. PubMed:16679305

Annotations
Experimental Factor Ontology (EFO)
NIH-3T3 cell
NCBI Taxonomy Ids
10090

p(HGNC:KRAS, var(p.Gly12Val)) prognosticBiomarkerFor path(MESHD:Recurrence)

K-Ras Asp12 (K12D) is more prevalent in benign than in malignant human colorectal tumors, whereas K-Ras Val12 (K12V) associates with more advanced and metastatic carcinomas, higher recurrence and decreased survival. PubMed:16679305

Annotations
MeSH
Colorectal Neoplasms
NCBI Taxonomy Ids
9606

p(HGNC:KRAS, var(p.Gly12Val)) increases p(HGNC:PCNA)

Finally, the higher growth rate of the K12V tumors associates with enhanced Rb phosphorylation, and PCNA and cyclin B upregulation, consistent with faster G1/S and G2/M transitions, without alteration of apoptotic regulation. PubMed:16679305

Annotations
Experimental Factor Ontology (EFO)
NIH-3T3 cell
NCBI Taxonomy Ids
10090

Sample Nodes

About

BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of the open source project, PyBEL. Please feel free to contact us here to give us feedback or report any issues.