GAP: A graphical environment for matrix visualization and cluster analysis

Wu, Hanming; Tien, Yong Ming; Chen, Chun-Houh

doi:10.1016/j.csda.2008.09.029

Cited by 99 publications

(76 citation statements)

References 21 publications

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“…Rich features with complex WIMP user interface: GAP [60], PermutMatrix [15], Voyager [17,46], VisuLab [34], T alK [29], and AMADO [14] generally support most of the requirements: R1, R2 to some extent, R3, R4, R5, and for PermutMatrix [15], R6. In contrast with previous systems, they provide table layout features and support the reordering of subsets, hence a better support for R4 and R5.…”

Section: Computer Adaptations Of Bertin's Methodsmentioning

confidence: 99%

Revisiting Bertin Matrices: New Interactions for Crafting Tabular Visualizations

Périn

Dragicevic

Fekete

2014

IEEE Trans. Visual. Comput. Graphics

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This is the accepted version of the paper.This version of the publication may differ from the final published version. Abstract-We present BERTIFIER, a web app for rapidly creating tabular visualizations from spreadsheets. BERTIFIER draws from Jacques Bertin's matrix analysis method, whose goal was to "simplify without destroying" by encoding cell values visually and grouping similar rows and columns. Although there were several attempts to bring this method to computers, no implementation exists today that is both exhaustive and accessible to a large audience. BERTIFIER remains faithful to Bertin's method while leveraging the power of today's interactive computers. Tables are formatted and manipulated through crossets, a new interaction technique for rapidly applying operations on rows and columns. We also introduce visual reordering, a semi-interactive reordering approach that lets users apply and tune automatic reordering algorithms in a WYSIWYG manner. Sessions with eight users from different backgrounds suggest that BERTIFIER has the potential to bring Bertin's method to a wider audience of both technical and non-technical users, and empower them with data analysis and communication tools that were so far only accessible to a handful of specialists. Permanent repository link

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Section: Computer Adaptations Of Bertin's Methodsmentioning

confidence: 99%

Revisiting Bertin Matrices: New Interactions for Crafting Tabular Visualizations

Périn

Dragicevic

Fekete

2014

IEEE Trans. Visual. Comput. Graphics

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“…The heat maps of 365 miRNAs in terms of the proportion of infants in each group with detectable expression are illustrated in Figure 1, using the Generalized Association Plots program. 35 For 210 detectable miRNAs, the expression levels did not differ between the subjects with versus without BPD. When miRNA expression was dichotomized as detectable or not, differential detectability between groups was found in 4 miRNAs.…”

Section: Mirnas Identified From the Older-age Setmentioning

confidence: 99%

MicroRNA Expression Aberration Associated with Bronchopulmonary Dysplasia in Preterm Infants: A Preliminary Study

Wu¹,

Chen²,

Hsieh³

et al. 2013

Respir Care

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BACKGROUND: Because environmental insults and genetic factors account for the variance in the risk of bronchopulmonary dysplasia (BPD) in very low birth weight (VLBW, birth weight < 1,500 g) preterm infants, the search for BPD biomarkers has begun to focus on the regulators of non-coding RNA such as microRNAs (miRNAs). Therefore, this study aimed to identify potential miRNAs involved in the pathogenesis of BPD in VLBW preterm infants. METHODS: A case-control study (15 subjects with BPD and 15 sex-matched control subjects without BPD) was conducted to investigate the expression profiles of 365 miRNAs in the peripheral blood of VLBW preterm infants at 36 weeks post-menstrual age (called the older-age set). The expression levels of identified miRNAs were further evaluated in a subsample of blood collected during the first 2 weeks post-natal age (called the younger-age set). Possible biological functions and pathways implicated in the target genes regulated by the miRNAs were explored using database predictions. RESULTS: A 4-miRNA signature (miR-152, miR-30a-3p, miR-133b, and miR-7) with aberrant expression levels at 36 weeks, derived from a supervised classification with internal cross-validation, discriminated the subjects with BPD from those without BPD with an accuracy of 0.91. The discriminative accuracy of the 4 miRNAs was supported by random permutations of either the disease status or the number of miRNAs selected (both P < .001). A down-regulation change of miR-152 and miR-30a-3p expression levels and an up-regulation change of miR-133b and miR-7 expression levels were found in the older-age set, compared to the younger-age set. CONCLUSIONS: This is the first study to identify blood-based miRNAs associated with BPD. The findings provide information regarding the roles of these biomarkers in the development of BPD in VLBW preterm infants.

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“…Data is often represented in a matrix form, and research community has developed numerous methods for matrix visualization (Chen et al 2004;Wu et al 2010). In this contribution, we use banded matrices to visualize the data and the results of a data mining process in a way that the results become easily understandable to the domain specialist.…”

Section: Data Clustering and Visualization Using Banded Matricesmentioning

confidence: 99%

Explaining mixture models through semantic pattern mining and banded matrix visualization

et al. 2016

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This paper presents an approach to semi-automated data analysis, supported by tools for pattern construction, exploration and explanation. The proposed three-part methodology for multiresolution 0-1 data analysis consists of data clustering with mixture models, extraction of rules from clusters, as well as data and rule visualization using banded matrices. The results of the three-part process: clusters, rules from clusters, and banded structure of the data matrix are finally merged in a unified visual banded matrix display. The incorporation of multiresolution data is enabled by the supporting ontology, describing the relationships between the different resolutions, which is used as background knowledge in the semantic pattern mining process of descriptive rule induction. The presented experimental use case highlights the usefulness of the proposed methodology for analyzing complex DNA copy number amplification data, studied in previous research, for which we provide new insights in terms of induced semantic patterns and cluster/pattern visualization. The methodology is

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GAP: A graphical environment for matrix visualization and cluster analysis

Cited by 99 publications

References 21 publications

Revisiting Bertin Matrices: New Interactions for Crafting Tabular Visualizations

Revisiting Bertin Matrices: New Interactions for Crafting Tabular Visualizations

MicroRNA Expression Aberration Associated with Bronchopulmonary Dysplasia in Preterm Infants: A Preliminary Study

Explaining mixture models through semantic pattern mining and banded matrix visualization

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