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Interactive visual analysis of time-series microarray data
2008
The Visual Computer
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Estimating dynamic regulatory pathways using DNA microarray time-series can provide invaluable information about the dynamic interactions among genes and result in new methods of rational drug design. ...
In this paper, we present a unified modeling and visual approach focusing on visual analysis of gene regulatory pathways. ...
Also they do not fully support analysis of time-series microarray data. ...
doi:10.1007/s00371-007-0205-9
fatcat:p3weznvzkbd4xbu7kfpvfsisqy
Mayday - integrative analytics for expression data
2010
BMC Bioinformatics
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Mayday is an open source platform with emphasis on visual data exploration and analysis. ...
The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. ...
FB performed the data analysis and wrote the manuscript. KN coordinated and designed the study. All authors read and approved the final manuscript. ...
doi:10.1186/1471-2105-11-121
pmid:20214778
pmcid:PMC2848234
fatcat:6rcoyqif25eujgqx2df22jdsvy
GeneShelf: A Web-based Visual Interface for Large Gene Expression Time-Series Data Repositories
2009
IEEE Transactions on Visualization and Computer Graphics
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However, current gene expression data repositories provide static representations of the data and support limited interactions. ...
It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts. ...
We first present the background about microarray data analysis, visualizations for gene expression data, and tabular visualization techniques. ...
doi:10.1109/tvcg.2009.146
pmid:19834153
fatcat:bd36yl5bove7zomiyccusdggsu
Integrated Microbial Survey Analysis of Prokaryotic Communities for the PhyloChip Microarray
2010
Applied and Environmental Microbiology
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PhyloTrac is an integrated desktop application for analysis of PhyloChip microarray data. ...
PhyloTrac combined with PhyloChip provides turnkey and comprehensive identification and analysis of bacterial and archaeal communities in complex environmental samples. ...
Visualization and analysis. In addition to standardizing the scoring of PhyloChip microarray data, PhyloTrac provides powerful visualization and analysis features for exploring microbial diversity. ...
doi:10.1128/aem.00303-10
pmid:20581189
pmcid:PMC2918976
fatcat:dbdbkaocxjbvrgxe5fg3o5jypq
An Insight-Based Methodology for Evaluating Bioinformatics Visualizations
2005
IEEE Transactions on Visualization and Computer Graphics
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The results of the study guide biologists in selecting a visualization tool based on the type of their microarray data, visualization designers on the key role of user interaction techniques, and evaluators ...
In response, a wide variety of visualization tools have been created to facilitate data analysis. A primary purpose of these tools is to provide biologically relevant insight into the data. ...
They also thank Hideo Goto, Yoshi Kawaoka, and John Yin for assistance related to mRNA extraction, as well as Jeff Furlong and Emily Baechler for assistance with data sets. ...
doi:10.1109/tvcg.2005.53
pmid:16138554
fatcat:7f3duki22vahfcgrvbqfbnuckm
Dynamic querying for pattern identification in microarray and genomic data
2003
2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698)
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Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. ...
TimeSearcher can be used to interactively search these data sets for genes with expression profiles of interest. ...
Thanks to Steven Salzberg from The Institute for Genomics Research for providing the nucleotide sequence data. ...
doi:10.1109/icme.2003.1221346
dblp:conf/icmcs/HochheiserBMS03
fatcat:joc3qvhkmzejvc2iv7547otq3a
Interactive Visualization of Gene Regulatory Networks with Associated Gene Expression Time Series Data
[chapter]
2008
Mathematics and Visualization
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Mining the time-series data starts with a visual exploration of the whole interaction network. ...
Osprey cannot overlay time series expression data on the interaction network. Cytoscape [SMO + 03] is a popular data analysis tool, which does support visualization of gene expression attributes. ...
doi:10.1007/978-3-540-72630-2_17
fatcat:dnxg265j3ffovggc3nuqmsyy2q
Towards human-computer synergetic analysis of large-scale biological data
2013
BMC Bioinformatics
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The first, called XMAS (Experiential Microarray Analysis System) is designed for analysis of time-series transcriptional data. ...
This paradigm combines information visualization and human-computer interaction with algorithms for exploratory analysis of large-scale and complex data. ...
This article has been published as part of BMC Bioinformatics Volume 14 Supplement 14, 2013: Proceedings of the Tenth Annual MCBIOS Conference. Discovery in a sea of data. ...
doi:10.1186/1471-2105-14-s14-s10
pmid:24267485
pmcid:PMC3851181
fatcat:wckvtlgrlvde3iglffqfu6edxi
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks
2010
Bioinformatics
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It allows to interactively explore regulatory interactions in differentially expressed gene sets, occurring in collections of gene expression data (e.g. time series), obtained by microarrays or RNA-seq ...
Our plugin also provides a method for visualization of time series data, because Cytoscape offers only basic support by coloring nodes (genes) based on a single time point. ...
doi:10.1093/bioinformatics/btq535
pmid:20861033
pmcid:PMC2971575
fatcat:ev54zoe6draojjm6reu4pmuicq
Visualizing Temporal Dynamics at the Genomic and Metabolic Level
2009
2009 13th International Conference Information Visualisation
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We present an application for integrated visualization of gene expression data from time series experiments in gene regulation networks and metabolic networks. ...
Our application can (i) visualize the data from time series experiments in the context of a regulatory network and a metabolic network; (ii) identify and visualize active regulatory subnetworks from the ...
The combination of visual exploration of a time series in multiple contexts and statistical tests for analysis is powerful, and it speeds up the data analysis process. ...
doi:10.1109/iv.2009.41
dblp:conf/iv/BourquiW09
fatcat:gz35nbw5qbfpjg3vlxgrzqjapi
GENOME-WIDE PATHWAY ANALYSIS AND VISUALIZATION USING GENE EXPRESSION DATA
2001
Biocomputing 2002
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We present an approach for visualization of c-DNA microarray gene expression data in metabolic and regulatory pathways using multi-resolution animation at different levels of detail. ...
Visualization of results for high performance computing pose special problems due to the complexity and the volume of data these systems manipulate. ...
For example, in case of microarray time series data, this represents the time lapse between experiments t and t-1; in case of microarray experiments performed over increasing temperature levels, this represents ...
doi:10.1142/9789812799623_0043
fatcat:xxlczfbq6ra6nckqwqikj2zgd4
CbGRiTS: Cerebellar gene regulation in time and space
2015
Developmental Biology
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We present three analytical approaches that take advantage of specific aspects of the time series for transcriptome analysis. ...
The temporal information from time series transcriptome analysis can serve as a potent source of associative information between developmental processes and regulatory genes. ...
(C) Hierarchical clustering analysis was performed on the C57BL/6J (B6) and DBA/2J (D2) time series cerebellum microarray data. ...
doi:10.1016/j.ydbio.2014.09.032
pmid:25446528
fatcat:hugec223yncpndoynwqhkapgm4
Animated Interval Scatter-Plot Views for the Exploratory Analysis of Large-Scale Microarray Time-Course Data
2005
Information Visualization
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context of microarray time-series analysis as a whole. ...
A significant obstacle to achieving effective analysis of microarray time-course is the combined scale and complexity of the data. ...
Conclusion We have developed a novel technique for the analysis of microarray timecourse data. ...
doi:10.1057/palgrave.ivs.9500101
fatcat:el665mntebbyhoxzvmxfhrhcw4
Genomic data visualization on the Web
2004
Bioinformatics
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Prism is a Web-based software tool for generating annotated heat map visualizations of genome-wide data quickly. ...
The heat map is a popular technique for visualizing such data, plotting the data on a two-dimensional grid and using a color scale to represent the magnitude of each matrix entry. ...
This plot shows time series data; for non-time series data, a histogram would be produced. return later to the same data set or share experimental results with a colleague. ...
doi:10.1093/bioinformatics/bth154
pmid:14988106
fatcat:6andmnjmnjgfpn37lxzcfaw3ku
GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data
2004
Bioinformatics
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Inferring genetic network architecture from time series data generated from high-throughput experimental technologies, such as cDNA microarray, can help us to understand the system behavior of living organisms ...
GeneNetwork enables a user to readily reconstruct genetic networks based on microarray data without having intimate knowledge of the mathematical models. ...
We gratefully acknowledge the support of the National Research Program for Genomic Medicine of National Science Council, Taiwan (NSC 91-3112-13-001-002 and NSC 92-3112-B-027-001). ...
doi:10.1093/bioinformatics/bth428
pmid:15271782
fatcat:fla6k44r2bdvpjwd36vsllhlsm
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