Genomic data visualization on the Web

Wu, Wei; Noble, William Stafford

doi:10.1093/bioinformatics/bth154

Cited by 15 publications

(10 citation statements)

References 3 publications

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“…(A) Heatmap representation [74] of 1,610 circadian-regulated genes shows peak expression occurs at all phases. High expression is depicted in red and low expression in blue.…”

Section: Resultsmentioning

confidence: 99%

“…Transcript abundance of 1,610 nuclear-encoded genes, corresponding to 10.4% of genes with detectable expression levels, had a greater than 95% probable correlation (pMMC-β < 0.05) to a cosine wave with a period between 19 and 29 h; these genes were called “circadian regulated.” The relative amplitude is defined as the ratio of β (a measure of absolute amplitude) to mean Model-Based Expression Index of the 12 time points. The heat map display in Figure 1A was generated using Prism [74], a Web-based genomic data visualization program (http://noble.gs.washington.edu/prism). …”

Section: Methodsmentioning

confidence: 99%

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The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis

2007

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The circadian clock plays a pervasive role in the temporal regulation of plant physiology, environmental responsiveness, and development. In contrast, the phytohormone auxin plays a similarly far-reaching role in the spatial regulation of plant growth and development. Went and Thimann noted 70 years ago that plant sensitivity to auxin varied according to the time of day, an observation that they could not explain. Here we present work that explains this puzzle, demonstrating that the circadian clock regulates auxin signal transduction. Using genome-wide transcriptional profiling, we found many auxin-induced genes are under clock regulation. We verified that endogenous auxin signaling is clock regulated with a luciferase-based assay. Exogenous auxin has only modest effects on the plant clock, but the clock controls plant sensitivity to applied auxin. Notably, we found both transcriptional and growth responses to exogenous auxin are gated by the clock. Thus the circadian clock regulates some, and perhaps all, auxin responses. Consequently, many aspects of plant physiology not previously thought to be under circadian control may show time-of-day–specific sensitivity, with likely important consequences for plant growth and environmental responses.

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“…(A) Heatmap representation [74] of 1,610 circadian-regulated genes shows peak expression occurs at all phases. High expression is depicted in red and low expression in blue.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis

2007

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“…For instance, 'heatmap' is one of the most popular visualization techniques which can be used in bio-molecular expression data analysis. 45 Biomarkers' derivation based on 'heatmap'-like visualizations was also reported. 46 However, 'heatmap' and its applications in biomarker discovery organize expression values as matrix entries and analyze them by re-ordering the entries, which lose the information of the biomolecular context of these expression values.…”

Section: Discussionmentioning

confidence: 99%

Gene Terrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks

You

Fang

Chen

2008

Information Visualization

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We propose a new network visualization technique using scattered data interpolation and surface rendering, based upon a foundation layout of a scalar field. Contours of the interpolated surfaces are generated to support multi-scale visual interaction for data exploration. Our framework visualizes quantitative attributes of nodes in a network as a continuous surface by interpolating the scalar field, therefore avoiding scalability issues typical in conventional network visualizations while also maintaining the topological properties of the original network. We applied this technique to the study of a bio-molecular interaction network integrated with gene expression data for Alzheimer's Disease (AD). In this application, differential gene expression profiles obtained from the human brain are rendered for AD patients with differing degrees of severity and compared to healthy individuals. We show that this alternative visualization technique is effective in revealing several types of molecular biomarkers, which are traditionally difficult to detect due to 'noises' in data derived from DNA microarray experiments.

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“…Changes in the ambient conditions of complicated systems like galaxies, the stock market, or large meteorological phenomena can be readily displayed via differences in color or grayscale to assist investigators in hypothesis generating or data interpretation activities. Heat maps afford investigators the ability to study high-density data sets in a single visualization, while maintaining measurement relationships and data integrity [14][15][16].…”

Section: Introduction Backgroundmentioning

confidence: 99%

Quantification of Heat Map Data Displays for High-Throughput Analysis

Juneau¹

2015

J Pharmacogenomics Pharmacoproteomics

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Genomic data visualization on the Web

Cited by 15 publications

References 3 publications

The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis

The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis

Gene Terrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks

Quantification of Heat Map Data Displays for High-Throughput Analysis

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