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FunCoup specifications


Unique identifier OMICS_02888
Name FunCoup
Restrictions to use None
Maintained Yes

Publication for FunCoup

FunCoup citations


FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets

BMC Genomics
PMCID: 5836822
PMID: 29504895
DOI: 10.1186/s12864-018-4474-7

[…] c. have been developed – for example, KEGG PATHWAY [], BioCyc [], BioGRID [] and IntAct [].There are systems that allow the reconstruction of gene networks for a given set of genes/proteins including FunCoup [], STRING [], Pathway Studio [], Ingenuity Pathway Analysis [], PINA [], GeneMANIA [] and ReactomeFIViz []. These systems use various information sources on interactions of molecular genetic […]


The integration of weighted gene association networks based on information entropy

PLoS One
PMCID: 5741255
PMID: 29272314
DOI: 10.1371/journal.pone.0190029

[…] KEGG pathways, which support their functional coupling. Additionally, Alexeyenko et al mixed information derived from proteomics and genomics pipelines and generated a human gene association network FunCoup by an optimized Bayesian framework[]. Then, they used the network FunCoup to construct a protein-protein interaction network associated with the disease Alzheimer[]. STRING and FunCoup are sco […]


FunCoup 4: new species, data, and visualization

Nucleic Acids Res
PMCID: 5755233
PMID: 29165593
DOI: 10.1093/nar/gkx1138

[…] tion of proteins (,), understanding of cellular regulatory mechanisms (), pathway annotation (), gene prioritization, and disease gene discovery ().Several integrated global networks exist, including FunCoup (–), STRING (), GeneMANIA () and GIANT (). Although other ways to integrate data from various data sources are available, many networks use Bayesian techniques. FunCoup uses a unique redundanc […]


Characterization of potential driver mutations involved in human breast cancer by computational approaches

PMCID: 5564847
PMID: 28477017
DOI: 10.18632/oncotarget.17225

[…] er gene identification, we have also validated the genetic interactions through various approaches. To test the capability of identifying the driver genes in genetic interaction level, we constructed FunCoup (functional Coupling) database to explore the functional relationship between genes and their functions []. Genetic network is most significant method to derive genetic as well as functionally […]


GenePANDA—a novel network based gene prioritizing tool for complex diseases

Sci Rep
PMCID: 5333103
PMID: 28252032
DOI: 10.1038/srep43258

[…] s such as GenePANDA. Besides the STRING network, there are also a number of large-scale functional interaction networks that differ from STRING in their knowledge source and scoring strategy, such as Funcoup, PIPs, Genes2FANs, GeneMania and HEFalMp, etc. The integration of different functional interaction network, or the combination of predicted candidate disease genes using different networks may […]


CNV Analysis Associates AKNAD1 with Type 2 Diabetes in Jordan Subpopulations

Sci Rep
PMCID: 4543987
PMID: 26292654
DOI: 10.1038/srep13391

[…] es, and the pathway of type 2 diabetes showed evidence of nominal significance (). The identification of these pathways suggested the validity of our study. Furthermore, a similar network analysis in FunCoup 3.0 () yielded murine homologues of three genes (MAPK8IP3, RTN2, MMEL1), and two additional functional partners (Vapa and Ddost) in ER-related pathway ().CNVR chr1:109367944-109371874 covers n […]


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FunCoup institution(s)
Stockholm Bioinformatics Centre, Science for Life Laboratory, Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University and Swedish eScience Research Center, Sweden

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