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Genephony specifications


Unique identifier OMICS_17714
Name Genephony
Interface Web user interface
Restrictions to use None
Programming languages Java, Other
Computer skills Basic
Stability No
Maintained No

Publication for Genephony

Genephony citations


GenoSets: Visual Analytic Methods for Comparative Genomics

PLoS One
PMCID: 3463605
PMID: 23056299
DOI: 10.1371/journal.pone.0046401

[…] ining tools that can build these queries. The web tool Galaxy has been created to work with the UCSC Genome Browser. Galaxy uses the intersection of track information to categorize genes. Similarly, GenePhony is a tool that allows the user to construct queries as the intersection of multiple sets. However, in both cases, many steps of data manipulation are required both within and outside the in […]


A Knowledge Based Method for Association Studies on Complex Diseases

PLoS One
PMCID: 3435396
PMID: 22970175
DOI: 10.1371/journal.pone.0044162

[…] rizes the functional roles of the genotyped and validated SNPs related to the pathways under investigation. All procedures related to SNP set creation, manipulation and filtering were performed using Genephony, a user-friendly web-based browser for large-scale genomic datasets manipulation and for knowledge-based discovery tasks .Finally, to test if the association detected for RA-associated pathw […]


Whole Genome Sequences of a Male and Female Supercentenarian, Ages Greater than 114 Years

Front Genet
PMCID: 3262222
PMID: 22303384
DOI: 10.3389/fgene.2011.00090

[…] ng errors. After this annotation, approximately 1.5% of the SNPs from the original set that were not found in dbSNP or 1000 Genomes were labeled as “novel” (Figure A). These steps were conducted with Genephony, an online tool for the manipulation of large datasets of genomic information (Nuzzo and Riva, ). […]


Phenotypic and genotypic data integration and exploration through a web service architecture

BMC Bioinformatics
PMCID: 2762070
PMID: 19828081
DOI: 10.1186/1471-2105-10-S12-S5

[…] ply by expanding or collapsing the table rows and columns (Figure ).The next step is to retrieve a set of markers that are known to be related to the phenotypes. Through the automatic SOAP request to Genephony described above, the user can retrieve all the SNPs (if any) related to the OMIM entry associated with the phenotype under study. In this example, the dataset produced by Genephony in respon […]


Phenotype forecasting with SNPs data through gene based Bayesian networks

BMC Bioinformatics
PMCID: 2646249
PMID: 19208195
DOI: 10.1186/1471-2105-10-S2-S7

[…] nificant SNPs (p < 10-4, corrected for permutation tests). P-values given by genotypic association tests confirmed the same results as the allelic association tests.SNP annotation was performed using Genephony, an online tool for genomic dataset annotation []: a SNP is annotated to a gene if it is located in a 10 Kb region around the coding sequence. Selecting only those genes represented by at le […]

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Genephony institution(s)
Centre for Tissue Engineering, University of Pavia, Pavia, Italy; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
Genephony funding source(s)
This project was supported by NIH grant R01 HL87681-01, "Genome-Wide Association Studies in Sickle Cell Anemia and in Centenarians", by NIH grant 5U54LM008748- 02 (National Centers for Biomedical Computing), and by the "Bioinformatics for Tissue Engineering: Creation of an International Research Group" project, funded by Fondazione Cariplo.

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