Provenance

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miguel.angel.ibarra.arellano@scai-extern.fraunhofer.de at 2018-09-11 15:34:09
Authors
Miguel A. Ibarra-Arellano
Contact
miguel.angel.ibarra.arellano@scai-extern.fraunhofer.de
Description
Colorectal Cancer Knowledge Assembly with drug associations and Pathways.
License
Fraunhofer SCAI copyright
Copyright
Copyright (c) 2018, SCAI. All Rights Reserved.
Number Nodes
74
Number Edges
117
Number Components
10
Network Density
0.0216586
Average Degree
1.58108
Number Citations
22
Number BEL Errors
276

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
Colorectal Cancer Model v2.0.6 92%
CRC_combined v1.1 85%
CRC_combined.bel v1.0 80%
BEL Framework Large Corpus Document v20170611 27%
Selventa Protein Families Definitions v20150611 19%
BEL Framework Small Corpus Document v20150611 16%
fc34ba14-6a91-4142-811b-cacad7ad64ce_3150.txt v1.0 15%
BEL Framework Example 3 Document v2015611 14%
Test1 v1.1.1 12%
colorectal cancer Knowledge Assembly - Drugs v1.0.1 11%

Sample Edges

g(HGNC:FCGR1CP) association bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity")

SNPs in genes encoding Fcγ receptors are functionally relevant to cetuximab-mediated ADCC in colorectal cancer PubMed:26817995

Annotations
Experimental Factor Ontology (EFO)
HCT-15 cell
Disease Ontology (DO)
colorectal cancer

path(MESHD:Leukopenia) positiveCorrelation a(CHEBI:irinotecan)

Ad libitum fed animals developed leucopenia compared with untreated controls, whereas fasted mice did not. PubMed:26332723

Annotations
NCBI Taxonomy Ids
10090
Experimental Factor Ontology (EFO)
LS174T
Disease Ontology (DO)
colorectal cancer

bp(GOBP:transport) association g(HGNC:ABCC10)

Model selection resulted in the inclusion of 14 SNPs from eight genes (six transporter genes, ABCA9, ABCB11, ABCC10, ATP1A1, ATP1B2, ATP8B3, and two metabolism genes GSTM5, GRHPR), which significantly improved model fit. Using bootstrap analysis we show an improvement of the prediction error of 3.7% in patients treated with oxaliplatin. Several variants in genes involved in metabolism and transport could thus be potential predictive markers for oxaliplatin treatment in CRC patients. PubMed:26835885

Annotations
Experimental Factor Ontology (EFO)
HCT-15 cell
Disease Ontology (DO)
colorectal cancer

bp(GOBP:transport) association g(HGNC:ATP1A1)

Model selection resulted in the inclusion of 14 SNPs from eight genes (six transporter genes, ABCA9, ABCB11, ABCC10, ATP1A1, ATP1B2, ATP8B3, and two metabolism genes GSTM5, GRHPR), which significantly improved model fit. Using bootstrap analysis we show an improvement of the prediction error of 3.7% in patients treated with oxaliplatin. Several variants in genes involved in metabolism and transport could thus be potential predictive markers for oxaliplatin treatment in CRC patients. PubMed:26835885

Annotations
Experimental Factor Ontology (EFO)
HCT-15 cell
Disease Ontology (DO)
colorectal cancer

bp(GOBP:transport) association g(HGNC:ATP8B3)

Model selection resulted in the inclusion of 14 SNPs from eight genes (six transporter genes, ABCA9, ABCB11, ABCC10, ATP1A1, ATP1B2, ATP8B3, and two metabolism genes GSTM5, GRHPR), which significantly improved model fit. Using bootstrap analysis we show an improvement of the prediction error of 3.7% in patients treated with oxaliplatin. Several variants in genes involved in metabolism and transport could thus be potential predictive markers for oxaliplatin treatment in CRC patients. PubMed:26835885

Annotations
Experimental Factor Ontology (EFO)
HCT-15 cell
Disease Ontology (DO)
colorectal cancer

Sample Nodes

p(HGNC:AKT1)

In-Edges: 267 | Out-Edges: 239 | Explore Neighborhood | Download JSON

bp(GOBP:"apoptotic process")

In-Edges: 916 | Out-Edges: 234 | Classes: 1 | Children: 2 | Explore Neighborhood | Download JSON

p(HGNC:MAPK3)

In-Edges: 451 | Out-Edges: 274 | Explore Neighborhood | Download JSON

path(MESHD:Neoplasms)

In-Edges: 413 | Out-Edges: 222 | Explore Neighborhood | Download JSON

p(HGNC:FCGR2B)

In-Edges: 6 | Out-Edges: 6 | Explore Neighborhood | Download JSON

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.