GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks

Shoshi A, Hofestädt R, Zolotareva O, Friedrichs M, Maier A, Ivanisenko VA, Dosenko VE, Bragina EY (2018)
JOURNAL OF INTEGRATIVE BIOINFORMATICS 15(4): 20180049.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Shoshi, AlbanUniBi; Hofestädt, RalfUniBi; Zolotareva, OlgaUniBi; Friedrichs, MarcelUniBi ; Maier, Alex; Ivanisenko, Vladimir A.; Dosenko, Victor E.; Bragina, Elena Yu
Abstract / Bemerkung
The prevalence of comorbid diseases poses a major health issue for millions of people worldwide and an enormous socio-economic burden for society. The molecular mechanisms for the development of comorbidities need to be investigated. For this purpose, a workflow system was developed to aggregate data on biomedical entities from heterogeneous data sources. The process of integrating and merging all data sources of the workflow system was implemented as a semi-automatic pipeline that provides the import, fusion, and analysis of the highly connected biomedical data in a Neo4j database GenCoNet. As a starting point, data on the common comorbid diseases essential hypertension and bronchial asthma was integrated. GenCoNet (https: / /genconet.kalis-amts.de) is a curated database that provides a better understanding of hereditary bases of comorbidities.
Erscheinungsjahr
2018
Zeitschriftentitel
JOURNAL OF INTEGRATIVE BIOINFORMATICS
Band
15
Ausgabe
4
Art.-Nr.
20180049
ISSN
1613-4516
Page URI
https://pub.uni-bielefeld.de/record/2933313

Zitieren

Shoshi A, Hofestädt R, Zolotareva O, et al. GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. JOURNAL OF INTEGRATIVE BIOINFORMATICS. 2018;15(4): 20180049.
Shoshi, A., Hofestädt, R., Zolotareva, O., Friedrichs, M., Maier, A., Ivanisenko, V. A., Dosenko, V. E., et al. (2018). GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. JOURNAL OF INTEGRATIVE BIOINFORMATICS, 15(4), 20180049. doi:10.1515/jib-2018-0049
Shoshi, Alban, Hofestädt, Ralf, Zolotareva, Olga, Friedrichs, Marcel, Maier, Alex, Ivanisenko, Vladimir A., Dosenko, Victor E., and Bragina, Elena Yu. 2018. “GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks”. JOURNAL OF INTEGRATIVE BIOINFORMATICS 15 (4): 20180049.
Shoshi, A., Hofestädt, R., Zolotareva, O., Friedrichs, M., Maier, A., Ivanisenko, V. A., Dosenko, V. E., and Bragina, E. Y. (2018). GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. JOURNAL OF INTEGRATIVE BIOINFORMATICS 15:20180049.
Shoshi, A., et al., 2018. GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. JOURNAL OF INTEGRATIVE BIOINFORMATICS, 15(4): 20180049.
A. Shoshi, et al., “GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks”, JOURNAL OF INTEGRATIVE BIOINFORMATICS, vol. 15, 2018, : 20180049.
Shoshi, A., Hofestädt, R., Zolotareva, O., Friedrichs, M., Maier, A., Ivanisenko, V.A., Dosenko, V.E., Bragina, E.Y.: GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. JOURNAL OF INTEGRATIVE BIOINFORMATICS. 15, : 20180049 (2018).
Shoshi, Alban, Hofestädt, Ralf, Zolotareva, Olga, Friedrichs, Marcel, Maier, Alex, Ivanisenko, Vladimir A., Dosenko, Victor E., and Bragina, Elena Yu. “GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks”. JOURNAL OF INTEGRATIVE BIOINFORMATICS 15.4 (2018): 20180049.

24 References

Daten bereitgestellt von Europe PubMed Central.

Asthma Genetics in the Post-GWAS Era.
Ober C., Ann Am Thorac Soc 13 Suppl 1(), 2016
PMID: 27027959
Probing genetic overlap among complex human phenotypes.
Rzhetsky A, Wajngurt D, Park N, Zheng T., Proc. Natl. Acad. Sci. U.S.A. 104(28), 2007
PMID: 17609372
Evolutionary history of human disease genes reveals phenotypic connections and comorbidity among genetic diseases.
Park S, Yang JS, Kim J, Shin YE, Hwang J, Park J, Jang SK, Kim S., Sci Rep 2(), 2012
PMID: 23091697
30-year trends in asthma and the trends in relation to hospitalization and mortality.
Pelkonen MK, Notkola IK, Laatikainen TK, Jousilahti P., Respir Med 142(), 2018
PMID: 30170798
Allergic respiratory disease as a potential co-morbidity for hypertension.
Aung T, Bisognano JD, Morgan MA., Cardiol J 17(5), 2010
PMID: 20865673
Drug-disease and drug-drug interactions: systematic examination of recommendations in 12 UK national clinical guidelines.
Dumbreck S, Flynn A, Nairn M, Wilson M, Treweek S, Mercer SW, Alderson P, Thompson A, Payne K, Guthrie B., BMJ 350(), 2015
PMID: 25762567
DrugCentral: online drug compendium.
Ursu O, Holmes J, Knockel J, Bologa CG, Yang JJ, Mathias SL, Nelson SJ, Oprea TI., Nucleic Acids Res. 45(D1), 2016
PMID: 27789690
InterMine: extensive web services for modern biology.
Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stepan R, Sullivan J, Micklem G., Nucleic Acids Res. 42(Web Server issue), 2014
PMID: 24753429
Developing integrated crop knowledge networks to advance candidate gene discovery.
Hassani-Pak K, Castellote M, Esch M, Hindle M, Lysenko A, Taubert J, Rawlings C., Appl Transl Genom 11(), 2016
PMID: 28018846
DrugBank 5.0: a major update to the DrugBank database for 2018.
Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, Wilson M., Nucleic Acids Res. 46(D1), 2018
PMID: 29126136
The ChEMBL database in 2017.
Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrian-Uhalte E, Davies M, Dedman N, Karlsson A, Magarinos MP, Overington JP, Papadatos G, Smit I, Leach AR., Nucleic Acids Res. 45(D1), 2016
PMID: 27899562
Ondex Web: web-based visualization and exploration of heterogeneous biological networks.
Taubert J, Hassani-Pak K, Castells-Brooke N, Rawlings CJ., Bioinformatics 30(7), 2013
PMID: 24363379
Systematic integration of biomedical knowledge prioritizes drugs for repurposing.
Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE., Elife 6(), 2017
PMID: 28936969
Annotating the human genome with Disease Ontology.
Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL., BMC Genomics 10 Suppl 1(), 2009
PMID: 19594883
The Human Phenotype Ontology in 2017.
Kohler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Ayme S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jahn JA, James R, Krause R, F Laulederkind SJ, Lochmuller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Zuchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN., Nucleic Acids Res. 45(D1), 2016
PMID: 27899602
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search.
Rappaport N, Twik M, Plaschkes I, Nudel R, Iny Stein T, Levitt J, Gershoni M, Morrey CP, Safran M, Lancet D., Nucleic Acids Res. 45(D1), 2016
PMID: 27899610
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants.
Pinero J, Bravo A, Queralt-Rosinach N, Gutierrez-Sacristan A, Deu-Pons J, Centeno E, Garcia-Garcia J, Sanz F, Furlong LI., Nucleic Acids Res. 45(D1), 2016
PMID: 27924018
A meta-analysis of gene expression signatures of blood pressure and hypertension.
Huan T, Esko T, Peters MJ, Pilling LC, Schramm K, Schurmann C, Chen BH, Liu C, Joehanes R, Johnson AD, Yao C, Ying SX, Courchesne P, Milani L, Raghavachari N, Wang R, Liu P, Reinmaa E, Dehghan A, Hofman A, Uitterlinden AG, Hernandez DG, Bandinelli S, Singleton A, Melzer D, Metspalu A, Carstensen M, Grallert H, Herder C, Meitinger T, Peters A, Roden M, Waldenberger M, Dorr M, Felix SB, Zeller T; International Consortium for Blood Pressure GWAS (ICBP), Vasan R, O'Donnell CJ, Munson PJ, Yang X, Prokisch H, Volker U, van Meurs JB, Ferrucci L, Levy D., PLoS Genet. 11(3), 2015
PMID: 25785607
A Severe Asthma Disease Signature from Gene Expression Profiling of Peripheral Blood from U-BIOPRED Cohorts.
Bigler J, Boedigheimer M, Schofield JPR, Skipp PJ, Corfield J, Rowe A, Sousa AR, Timour M, Twehues L, Hu X, Roberts G, Welcher AA, Yu W, Lefaudeux D, Meulder B, Auffray C, Chung KF, Adcock IM, Sterk PJ, Djukanovic R; U-BIOPRED Study Group ‖., Am. J. Respir. Crit. Care Med. 195(10), 2017
PMID: 27925796
Systematic identification of trans eQTLs as putative drivers of known disease associations.
Westra HJ, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, Christiansen MW, Fairfax BP, Schramm K, Powell JE, Zhernakova A, Zhernakova DV, Veldink JH, Van den Berg LH, Karjalainen J, Withoff S, Uitterlinden AG, Hofman A, Rivadeneira F, Hoen PAC', Reinmaa E, Fischer K, Nelis M, Milani L, Melzer D, Ferrucci L, Singleton AB, Hernandez DG, Nalls MA, Homuth G, Nauck M, Radke D, Volker U, Perola M, Salomaa V, Brody J, Suchy-Dicey A, Gharib SA, Enquobahrie DA, Lumley T, Montgomery GW, Makino S, Prokisch H, Herder C, Roden M, Grallert H, Meitinger T, Strauch K, Li Y, Jansen RC, Visscher PM, Knight JC, Psaty BM, Ripatti S, Teumer A, Frayling TM, Metspalu A, van Meurs JBJ, Franke L., Nat. Genet. 45(10), 2013
PMID: 24013639
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).
MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H., Nucleic Acids Res. 45(D1), 2016
PMID: 27899670
dbSNP: the NCBI database of genetic variation.
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K., Nucleic Acids Res. 29(1), 2001
PMID: 11125122
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 30864352
PubMed | Europe PMC

Suchen in

Google Scholar