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Information


Unique identifier OMICS_29224
Name GAP
Alternative name Generalized Association Plots
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Windows
Programming languages Java
Computer skills Medium
Version 0.2.7
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Chun-Houh Chen

Additional information


http://gap.stat.sinica.edu.tw/Software/GAP/Help.html/Installation/index.htm http://gap.stat.sinica.edu.tw/Software/GAP/Help.html/index.html

Publications for Generalized Association Plots

GAP citations

 (11)
library_books

A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters

2017
Sci Rep
PMCID: 5660162
PMID: 29079755
DOI: 10.1038/s41598-017-13297-0

[…] representing, respectively, the presence or absence of a specific PD in a specific species.Bi-clustering analysis (also known as co-clustering analysis) was then performed on the binary matrix using Generalized Association Plots (GAP), a tool for matrix visualization and clustering analysis. The Jaccard similarity coefficient is used to compute the distance (i.e. similarity) between any two matri […]

library_books

Using an Event History with Risk Free Model to Study the Genetics of Alcoholism

2017
Sci Rep
PMCID: 5434012
PMID: 28512340
DOI: 10.1038/s41598-017-01791-4

[…] ine the associations among the gene–environment strata fitted in Table , we plotted Fig.  to display the clustering of the three selected SNPs (genes) and habitual smoking of the 65 subjects by using Generalized association plots (GAP), . Considering the minor-allele carriers as risky revealed that GRIN2B (rs172677) highly overlaps with the habitual smoking status. In addition, smokers who carried […]

library_books

Resistin reinforces interferon λ 3 to eliminate hepatitis C virus with fine tuning from RETN single nucleotide polymorphisms

2016
Sci Rep
PMCID: 4967850
PMID: 27477870
DOI: 10.1038/srep30799

[…] rmined to narrow down the 10 RETN SNPs. The statistical significance of the genotype correlations was evaluated using linear-by-linear association. Visualization of the correlation was achieved using generalized association plots. The diagnostic accuracy of using pre-therapy resistin to predict therapeutic response was assessed in terms of true positive (sensitivity) versus true negative (1-specif […]

library_books

Functional Analysis and Characterization of Differential Coexpression Networks

2015
Sci Rep
PMCID: 4539605
PMID: 26282208
DOI: 10.1038/srep13295

[…] al similarity matrix was formed. Hierarchical agglomerative average-linkage clustering with the Pearson correlation coefficient as the distance metric was applied to the functional similarity matrix. Generalized Association Plots (GAP) were used to perform hierarchical clustering analysis and to view the results. The distance thresholds were determined based on the visual inspection of the heatmap […]

library_books

Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid Regulated Phosphorylation Dynamics in Arabidopsis

2015
BMC Genomics
PMCID: 4506601
PMID: 26187819
DOI: 10.1186/s12864-015-1753-4

[…] x values were z-transformed by following formula:z=x−μρThese z scores were then clustered by one-way hierarchical clustering by Pearson correlation coefficient and average linkage clustering in GAP (Generalized Association Plots) []. […]

library_books

Modulated expression of human peripheral blood microRNAs from infancy to adulthood and its role in aging

2014
Aging Cell
PMCID: 4326935
PMID: 24803090
DOI: 10.1111/acel.12225

[…] lation between differentially expressed miRNA and age in adults group. To help visualize the differential expression patterns, we adopted the method of matrix visualization using the software program Generalized Association Plots (Wu et al., ) to compare the miRNA expression levels between preterm infants and adults. The corresponding chromosomal locations of the miRNAs were retrieved from miRBase […]

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GAP institution(s)
Department of Statistics, National Taipei University, Taiwan, China; Digital Transformation Institute, Institute for Information Industry, Taiwan, China; Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taiwan, China; Department of Psychology, College of Public Health, Neurobiology and Cognitive Science Center, Taiwan, China; Institute of Biomedical Sciences, Academia Sinica, Taiwan, China; Institute of Statistical Science, Academia Sinica, Taiwan, China
GAP funding source(s)
Supported by grants from the Ministry of Science and Technology of Taiwan, China under the grant NSC 97-2118-M-032-001, NSC 98-3112-B-001-027 and NSC 99-3112-B-001-029 in the National Research Program for Genomic Medicine.

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