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Interactive visual analysis of time-series microarray data

Dong Hyun Jeong, Alireza Darvish, Kayvan Najarian, Jing Yang, William Ribarsky
2008 The Visual Computer  
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

Florian Battke, Stephan Symons, Kay Nieselt
2010 BMC Bioinformatics  
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

Bohyoung Kim, Bongshin Lee, S. Knoblach, E. Hoffman, Jinwook Seo
2009 IEEE Transactions on Visualization and Computer Graphics  
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

M. C. Schatz, A. M. Phillippy, P. Gajer, T. Z. DeSantis, G. L. Andersen, J. Ravel
2010 Applied and Environmental Microbiology  
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

P. Saraiya, C. North, K. Duca
2005 IEEE Transactions on Visualization and Computer Graphics  
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

H. Hochheiser, E.H. Baehrecke, S.M. Mount, B. Shneiderman
2003 2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698)  
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]

Michel A. Westenberg, Sacha A. F. T. van Hijum, Andrzej T. Lulko, Oscar P. Kuipers, Jos B. T. M. Roerdink
2008 Mathematics and Visualization  
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

Rahul Singh, Hui Yang, Ben Dalziel, Daniel Asarnow, William Murad, David Foote, Matthew Gormley, Jonathan Stillman, Susan Fisher
2013 BMC Bioinformatics  
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

M. A. Westenberg, J. B. T. M. Roerdink, O. P. Kuipers, S. A. F. T. van Hijum
2010 Bioinformatics  
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

Romain Bourqui, Michel A. Westenberg
2009 2009 13th International Conference Information Visualisation  
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

M. P. KURHEKAR, S. ADAK, S. JHUNJHUNWALA, K. RAGHUPATHY
2001 Biocomputing 2002  
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

Thomas Ha, Douglas Swanson, Matt Larouche, Randy Glenn, Dave Weeden, Peter Zhang, Kristin Hamre, Michael Langston, Charles Phillips, Mingzhou Song, Zhengyu Ouyang, Elissa Chesler (+8 others)
2015 Developmental Biology  
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

Paul Craig, Jessie Kennedy, Andrew Cumming
2005 Information Visualization  
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

W. Wu, W. S. Noble
2004 Bioinformatics  
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

C.-C. Wu, H.-C. Huang, H.-F. Juan, S.-T. Chen
2004 Bioinformatics  
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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